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["Additional file 3. Genome alignment  statistics for chicken sequenced in this study."]
["Sample ID","Total Read","Total UnMapped","Total Mapped","%","Total Pair Mapped","Total Single Mapped","Unique Mapped","Multi-Mapped","Perfect Mapped","Mismatch Mapped","Duplicate Reads"]
["GX01",75086772,"8831434-11.76%",66255338,{"v":0.8824,"d":"88.24%"},"65256217-86.91%","999121-1.33%","64694361-86.16%","1560977-2.08%","147854-0.2%","66107484-88.04%","2107562-2.81%"]
["GX03",100000000,"7045354-7.05%",92954646,{"v":0.9295,"d":"92.95%"},"89979496-89.98%","2975150-2.98%","87716536-87.72%","5238110-5.24%","217874-0.22%","92736772-92.74%","8828096-8.83%"]
["GX04",77741942,"8355789-10.75%",69386153,{"v":0.8925,"d":"89.25%"},"68543611-88.17%","842542-1.08%","67888105-87.32%","1498048-1.93%","138305-0.18%","69247848-89.07%","2163530-2.78%"]
["GX05",71292768,"7946095-11.15%",63346673,{"v":0.8885,"d":"88.85%"},"62648121-87.87%","698552-0.98%","61886277-86.81%","1460396-2.05%","101976-0.14%","63244697-88.71%","1985610-2.79%"]
["GX23",81671338,"10809214-13.24%",70862124,{"v":0.8676,"d":"86.76%"},"69885079-85.57%","977045-1.2%","69280043-84.83%","1582081-1.94%","116617-0.14%","70745507-86.62%","2462192-3.01%"]
["GX24",70408382,"7839384-11.13%",62568998,{"v":0.8887,"d":"88.87%"},"61706830-87.64%","862168-1.22%","61123169-86.81%","1445829-2.05%","117802-0.17%","62451196-88.7%","1848288-2.63%"]
["GX25",91436058,"10361721-11.33%",81074337,{"v":0.8867,"d":"88.67%"},"80054357-87.55%","1019980-1.12%","79108680-86.52%","1965657-2.15%","129425-0.14%","80944912-88.53%","2216698-2.42%"]
["GX26",85749390,"10442101-12.18%",75307289,{"v":0.8782,"d":"87.82%"},"74211679-86.54%","1095610-1.28%","73356150-85.55%","1951139-2.28%","127393-0.15%","75179896-87.67%","2364450-2.76%"]
["GX28",89804190,"16004710-17.82%",73799480,{"v":0.8218,"d":"82.18%"},"72882721-81.16%","916759-1.02%","72045867-80.23%","1753613-1.95%","108663-0.12%","73690817-82.06%","1732966-1.93%"]
["GX32",92417292,"11548118-12.5%",80869174,{"v":0.875,"d":"87.50%"},"80034320-86.6%","834854-0.9%","78920947-85.4%","1948227-2.11%","106245-0.11%","80762929-87.39%","2440608-2.64%"]
["HB01",81676928,"10599440-12.98%",71077488,{"v":0.8702,"d":"87.02%"},"68848980-84.29%","2228508-2.73%","69016808-84.5%","2060680-2.52%","145508-0.18%","70931980-86.84%","2947058-3.61%"]
["HB02",80673716,"11457772-14.2%",69215944,{"v":0.858,"d":"85.80%"},"68160299-84.49%","1055645-1.31%","67241261-83.35%","1974683-2.45%","91996-0.11%","69123948-85.68%","2128468-2.64%"]
["HB06",82580724,"10386994-12.58%",72193730,{"v":0.8742,"d":"87.42%"},"71087465-86.08%","1106265-1.34%","70239920-85.06%","1953810-2.37%","91469-0.11%","72102261-87.31%","2171208-2.63%"]
["HB09",104511214,"12918088-12.36%",91593126,{"v":0.8764,"d":"87.64%"},"90260640-86.36%","1332486-1.27%","89183344-85.33%","2409782-2.31%","112036-0.11%","91481090-87.53%","2673822-2.56%"]
["HB11",105826398,"15275812-14.43%",90550586,{"v":0.8557,"d":"85.57%"},"89521982-84.59%","1028604-0.97%","88252941-83.39%","2297645-2.17%","191848-0.18%","90358738-85.38%","2184666-2.06%"]
["HB12",97200586,"15541358-15.99%",81659228,{"v":0.8401,"d":"84.01%"},"80799656-83.13%","859572-0.88%","79340091-81.63%","2319137-2.39%","120402-0.12%","81538826-83.89%","2309710-2.38%"]
["HB13",66278582,"7425036-11.2%",58853546,{"v":0.888,"d":"88.80%"},"57845641-87.28%","1007905-1.52%","57542053-86.82%","1311493-1.98%","79172-0.12%","58774374-88.68%","2218514-3.35%"]
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["HB27",74766744,"4260490-5.7%",70506254,{"v":0.943,"d":"94.30%"},"68360266-91.43%","2145988-2.87%","66852910-89.42%","3653344-4.89%","133994-0.18%","70372260-94.12%","8136654-10.88%"]
["HB29",87517578,"11725027-13.4%",75792551,{"v":0.866,"d":"86.60%"},"74916252-85.6%","876299-1%","73690264-84.2%","2102287-2.4%","99654-0.11%","75692897-86.49%","2002184-2.29%"]
["HL02",93389740,"11438063-12.25%",81951677,{"v":0.8775,"d":"87.75%"},"80893811-86.62%","1057866-1.13%","80017443-85.68%","1934234-2.07%","132568-0.14%","81819109-87.61%","2524094-2.7%"]
["HL03",92894378,"10398949-11.19%",82495429,{"v":0.8881,"d":"88.81%"},"81333602-87.55%","1161827-1.25%","80574094-86.74%","1921335-2.07%","131887-0.14%","82363542-88.66%","2334926-2.51%"]
["HL04",92068308,"10003717-10.87%",82064591,{"v":0.8913,"d":"89.13%"},"81118921-88.11%","945670-1.03%","80181815-87.09%","1882776-2.04%","149481-0.16%","81915110-88.97%","2411014-2.62%"]
["HL06",87081934,"11762747-13.51%",75319187,{"v":0.8649,"d":"86.49%"},"73687780-84.62%","1631407-1.87%","73464091-84.36%","1855096-2.13%","112762-0.13%","75206425-86.36%","2492436-2.86%"]
["HL10",117192200,"14909972-12.72%",102282228,{"v":0.8728,"d":"87.28%"},"99196274-84.64%","3085954-2.63%","99718035-85.09%","2564193-2.19%","175553-0.15%","102106675-87.13%","7037718-6.01%"]
["HL13",82943896,"10311894-12.43%",72632002,{"v":0.8757,"d":"87.57%"},"70768971-85.32%","1863031-2.25%","70909622-85.49%","1722380-2.08%","117615-0.14%","72514387-87.43%","2636578-3.18%"]
["HL16",89354552,"13911326-15.57%",75443226,{"v":0.8443,"d":"84.43%"},"73839733-82.64%","1603493-1.79%","73326118-82.06%","2117108-2.37%","107220-0.12%","75336006-84.31%","2416810-2.7%"]
["HL28",70788042,"10825192-15.29%",59962850,{"v":0.8471,"d":"84.71%"},"58803070-83.07%","1159780-1.64%","58441101-82.56%","1521749-2.15%","78675-0.11%","59884175-84.6%","1570554-2.22%"]
["HL30",100000000,"10288974-10.29%",89711026,{"v":0.8971,"d":"89.71%"},"86749624-86.75%","2961402-2.96%","85726084-85.73%","3984942-3.98%","183594-0.18%","89527432-89.53%","14419398-14.42%"]
["HL46",77156452,"9323742-12.08%",67832710,{"v":0.8792,"d":"87.92%"},"65856192-85.35%","1976518-2.56%","64557831-83.67%","3274879-4.24%","107100-0.14%","67725610-87.78%","7819940-10.14%"]
["HT01",80109138,"9696890-12.1%",70412248,{"v":0.879,"d":"87.90%"},"69455326-86.7%","956922-1.19%","68799123-85.88%","1613125-2.01%","170806-0.21%","70241442-87.68%","2087252-2.61%"]
["HT02",102150624,"13088579-12.81%",89062045,{"v":0.8719,"d":"87.19%"},"87766825-85.92%","1295220-1.27%","86719419-84.89%","2342626-2.29%","156394-0.15%","88905651-87.03%","2385412-2.34%"]
["HT10",79022198,"9073836-11.48%",69948362,{"v":0.8852,"d":"88.52%"},"69008751-87.33%","939611-1.19%","67959660-86%","1988702-2.52%","118454-0.15%","69829908-88.37%","3826450-4.84%"]
["HT13",100277000,"11239738-11.21%",89037262,{"v":0.8879,"d":"88.79%"},"87874418-87.63%","1162844-1.16%","86900560-86.66%","2136702-2.13%","149995-0.15%","88887267-88.64%","2607408-2.6%"]
["HT15",81358006,"9944814-12.22%",71413192,{"v":0.8778,"d":"87.78%"},"70434430-86.57%","978762-1.2%","69585005-85.53%","1828187-2.25%","119816-0.15%","71293376-87.63%","1769374-2.17%"]
["HT17",98868908,"12657946-12.8%",86210962,{"v":0.872,"d":"87.20%"},"84564330-85.53%","1646632-1.67%","83948625-84.91%","2262337-2.29%","160951-0.16%","86050011-87.03%","2418314-2.45%"]
["HT18",88656014,"11062029-12.48%",77593985,{"v":0.8752,"d":"87.52%"},"76294015-86.06%","1299970-1.47%","75700413-85.39%","1893572-2.14%","131977-0.15%","77462008-87.37%","2158000-2.43%"]
["HT22",96510312,"12489468-12.94%",84020844,{"v":0.8706,"d":"87.06%"},"82431247-85.41%","1589597-1.65%","81923196-84.89%","2097648-2.17%","141724-0.15%","83879120-86.91%","2511992-2.6%"]
["HT25",86035730,"10459699-12.16%",75576031,{"v":0.8784,"d":"87.84%"},"74404135-86.48%","1171896-1.36%","73770436-85.74%","1805595-2.1%","143168-0.17%","75432863-87.68%","2032926-2.36%"]
["HT26",78018498,"9645487-12.36%",68373011,{"v":0.8764,"d":"87.64%"},"67361808-86.34%","1011203-1.3%","66654380-85.43%","1718631-2.2%","125994-0.16%","68247017-87.48%","1906466-2.44%"]
["HX01",127089240,"20153046-15.86%",106936194,{"v":0.8414,"d":"84.14%"},"105762400-83.22%","1173794-0.92%","104403158-82.15%","2533036-1.99%","170634-0.13%","106765560-84.01%","2144166-1.69%"]
["HX03",83467552,"9978365-11.95%",73489187,{"v":0.8805,"d":"88.05%"},"72568865-86.94%","920322-1.1%","71532178-85.7%","1957009-2.34%","106282-0.13%","73382905-87.92%","2104580-2.52%"]
["HX05",81322772,"11106303-13.66%",70216469,{"v":0.8634,"d":"86.34%"},"69304988-85.22%","911481-1.12%","68483701-84.21%","1732768-2.13%","111710-0.14%","70104759-86.21%","1981048-2.44%"]
["HX13",85404942,"10794060-12.64%",74610882,{"v":0.8736,"d":"87.36%"},"73544380-86.11%","1066502-1.25%","72667548-85.09%","1943334-2.28%","104469-0.12%","74506413-87.24%","2147638-2.51%"]
["HX14",86046346,"11149103-12.96%",74897243,{"v":0.8704,"d":"87.04%"},"73996455-86%","900788-1.05%","72977828-84.81%","1919415-2.23%","104601-0.12%","74792642-86.92%","2182004-2.54%"]
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["HX31",77985100,"9165461-11.75%",68819639,{"v":0.8825,"d":"88.25%"},"68053834-87.27%","765805-0.98%","67082795-86.02%","1736844-2.23%","92754-0.12%","68726885-88.13%","1903114-2.44%"]
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