BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618670.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 1,244,357,534 number of mapped reads = 1,180,885,245 (94.9%) number of supplementary alignments = 3,698,017 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 596,152,269 number of mapped paired reads (second in pair) = 584,732,976 number of mapped paired reads (both in pair) = 1,156,589,366 number of mapped paired reads (singletons) = 24,295,879 number of mapped bases = 116,164,708,951 bp number of sequenced bases = 116,132,159,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,020,944 duplication rate = 23.66% >>>>>>> Insert size mean insert size = 44,333.9443 std insert size = 2,022,305.4033 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 53.5886 >>>>>>> ACTG content number of A's = 33,681,216,602 bp (29%) number of C's = 24,304,636,617 bp (20.93%) number of T's = 33,535,730,465 bp (28.88%) number of G's = 24,409,594,019 bp (21.02%) number of N's = 200,981,400 bp (0.17%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 1,243,899,460 number of insertions = 11,334,137 mapped reads with insertion percentage = 0.93% number of deletions = 14,092,530 mapped reads with deletion percentage = 1.16% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 37.5246X std coverageData = 386.1723X There is a 92.32% of reference with a coverageData >= 1X There is a 92.27% of reference with a coverageData >= 2X There is a 92.23% of reference with a coverageData >= 3X There is a 92.18% of reference with a coverageData >= 4X There is a 92.14% of reference with a coverageData >= 5X There is a 92.08% of reference with a coverageData >= 6X There is a 92.01% of reference with a coverageData >= 7X There is a 91.93% of reference with a coverageData >= 8X There is a 91.81% of reference with a coverageData >= 9X There is a 91.67% of reference with a coverageData >= 10X There is a 91.49% of reference with a coverageData >= 11X There is a 91.26% of reference with a coverageData >= 12X There is a 90.98% of reference with a coverageData >= 13X There is a 90.63% of reference with a coverageData >= 14X There is a 90.23% of reference with a coverageData >= 15X There is a 89.75% of reference with a coverageData >= 16X There is a 89.21% of reference with a coverageData >= 17X There is a 88.6% of reference with a coverageData >= 18X There is a 87.92% of reference with a coverageData >= 19X There is a 87.15% of reference with a coverageData >= 20X There is a 86.31% of reference with a coverageData >= 21X There is a 85.36% of reference with a coverageData >= 22X There is a 84.31% of reference with a coverageData >= 23X There is a 83.14% of reference with a coverageData >= 24X There is a 81.84% of reference with a coverageData >= 25X There is a 80.38% of reference with a coverageData >= 26X There is a 78.75% of reference with a coverageData >= 27X There is a 76.94% of reference with a coverageData >= 28X There is a 74.94% of reference with a coverageData >= 29X There is a 72.75% of reference with a coverageData >= 30X There is a 70.36% of reference with a coverageData >= 31X There is a 67.77% of reference with a coverageData >= 32X There is a 65% of reference with a coverageData >= 33X There is a 62.07% of reference with a coverageData >= 34X There is a 58.99% of reference with a coverageData >= 35X There is a 55.79% of reference with a coverageData >= 36X There is a 52.5% of reference with a coverageData >= 37X There is a 49.15% of reference with a coverageData >= 38X There is a 45.77% of reference with a coverageData >= 39X There is a 42.4% of reference with a coverageData >= 40X There is a 39.07% of reference with a coverageData >= 41X There is a 35.8% of reference with a coverageData >= 42X There is a 32.63% of reference with a coverageData >= 43X There is a 29.59% of reference with a coverageData >= 44X There is a 26.69% of reference with a coverageData >= 45X There is a 23.94% of reference with a coverageData >= 46X There is a 21.38% of reference with a coverageData >= 47X There is a 18.99% of reference with a coverageData >= 48X There is a 16.79% of reference with a coverageData >= 49X There is a 14.78% of reference with a coverageData >= 50X There is a 12.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9624259767 38.6127814983458 915.901255049503 chr2 243199373 9975035713 41.01587759027652 262.01084021808174 chr3 198022430 7670777522 38.73691238916723 31.15756497474721 chr4 191154276 7635526713 39.94431551716897 201.80180480663785 chr5 180915260 6985442558 38.61168238654937 33.717934519723876 chr6 171115067 6678242375 39.02778692772858 174.21973866697928 chr7 159138663 6320606743 39.717606167144936 285.79244225295355 chr8 146364022 5892882013 40.261820715749394 392.7853151139631 chr9 141213431 5023634181 35.574761872332104 417.9814806717748 chr10 135534747 6125701437 45.19653869276784 853.5342725579383 chr11 135006516 5413434924 40.09758257890308 214.26285800962637 chr12 133851895 5176465152 38.67308081069753 30.4418351021089 chr13 115169878 3680446108 31.956672802935504 22.151277096379832 chr14 107349540 3546802781 33.039757608649275 37.17917539523224 chr15 102531392 3376286788 32.9292982582349 23.130499728920814 chr16 90354753 3749621912 41.498889516083345 271.8024464076907 chr17 81195210 3345407250 41.20202718854967 184.5295322776011 chr18 78077248 3272765248 41.917015927610564 534.2071948700914 chr19 59128983 2456679023 41.54779768493566 406.6107487454756 chr20 63025520 2518644484 39.96229597153661 105.8065299539127 chr21 48129895 1645203692 34.18257388677038 200.63585644154097 chr22 51304566 1561497071 30.435830428816026 179.4728301439264 chrMT 16571 57286963 3457.0613119304808 551.9187423080939 chrX 155270560 3108249301 20.018278423160194 91.09275479969186 chrY 59373566 1323809232 22.296272923879965 401.04689951725896