BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617726.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 31,522,574 number of mapped reads = 30,737,749 (97.51%) number of supplementary alignments = 1,690,734 (5.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,540,650 number of mapped paired reads (second in pair) = 15,197,099 number of mapped paired reads (both in pair) = 30,240,908 number of mapped paired reads (singletons) = 496,841 number of mapped bases = 4,064,258,795 bp number of sequenced bases = 4,060,894,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,982,403 duplication rate = 20.67% >>>>>>> Insert size mean insert size = 393,580.7634 std insert size = 6,083,733.6279 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 52.5736 >>>>>>> ACTG content number of A's = 1,184,681,199 bp (29.17%) number of C's = 758,752,396 bp (18.68%) number of T's = 1,232,363,884 bp (30.35%) number of G's = 884,950,867 bp (21.79%) number of N's = 146,530 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 49,914,984 number of insertions = 810,659 mapped reads with insertion percentage = 2.47% number of deletions = 1,678,588 mapped reads with deletion percentage = 5.23% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 1.3129X std coverageData = 15.5716X There is a 38.54% of reference with a coverageData >= 1X There is a 24.92% of reference with a coverageData >= 2X There is a 16.5% of reference with a coverageData >= 3X There is a 11.47% of reference with a coverageData >= 4X There is a 8.08% of reference with a coverageData >= 5X There is a 5.83% of reference with a coverageData >= 6X There is a 4.26% of reference with a coverageData >= 7X There is a 3.16% of reference with a coverageData >= 8X There is a 2.37% of reference with a coverageData >= 9X There is a 1.8% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.07% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.66% of reference with a coverageData >= 14X There is a 0.53% of reference with a coverageData >= 15X There is a 0.42% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 311460388 1.2495872096543341 12.250069406488723 chr2 243199373 453888259 1.8663216660513349 18.135972809497975 chr3 198022430 275629526 1.3919106335580267 3.0570055334418296 chr4 191154276 186889805 0.9776909463432563 16.3101204974118 chr5 180915260 242507928 1.3404503743907508 2.8744774536963686 chr6 171115067 230148243 1.3449911047283756 6.37783992245512 chr7 159138663 218752138 1.3746008284611515 15.768589976056479 chr8 146364022 202148780 1.3811370939232595 5.038584818538282 chr9 141213431 214142011 1.516442235583101 25.32421709265218 chr10 135534747 220380428 1.6260068571198203 43.33358525022214 chr11 135006516 186329125 1.3801491255429479 11.606493661042244 chr12 133851895 164077476 1.2258136203450836 7.315977315841508 chr13 115169878 137241352 1.191642766175371 2.6043892402476976 chr14 107349540 118243144 1.1014778824389932 2.7863362740819735 chr15 102531392 111190192 1.0844502335440838 3.935922958978127 chr16 90354753 135322894 1.4976842889493593 26.16888188372791 chr17 81195210 85281736 1.0503296438299747 14.685243549182882 chr18 78077248 80527028 1.031376362035711 18.521109039315323 chr19 59128983 49281803 0.8334627199659429 6.842808020518524 chr20 63025520 105429103 1.6728002085504412 5.693668013691257 chr21 48129895 62628150 1.3012318019808686 8.482740125366055 chr22 51304566 22811494 0.44462892445089586 2.241960934771078 chrMT 16571 1349796 81.45531349948706 40.98460787817236 chrX 155270560 230437104 1.4841004244462055 5.714736978448543 chrY 59373566 18160892 0.30587504210206945 24.273910831735225