BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237292.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,503,472 number of mapped reads = 2,285,707 (91.3%) number of supplementary alignments = 12,161 (0.49%) number of secondary alignments = 0 number of mapped bases = 156,561,950 bp number of sequenced bases = 156,498,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,535 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1566 >>>>>>> ACTG content number of A's = 44,239,561 bp (28.27%) number of C's = 29,114,470 bp (18.6%) number of T's = 49,414,958 bp (31.58%) number of G's = 33,726,830 bp (21.55%) number of N's = 2,549 bp (0%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,125,008 number of insertions = 11,534 mapped reads with insertion percentage = 0.5% number of deletions = 36,016 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.18% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.4064X There is a 4.07% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9083195 0.03644201552460726 0.6472682039258616 chr2 243199373 10401413 0.04276907819166129 0.47882418068417404 chr3 198022430 10417996 0.05261018158397511 0.27302688455108975 chr4 191154276 7153014 0.037420109817475386 0.2443331437178052 chr5 180915260 8165144 0.04513242277074914 0.2565315350194802 chr6 171115067 17455116 0.10200805987470409 0.4628569966331023 chr7 159138663 10984319 0.06902357222895608 0.5104285378278454 chr8 146364022 7972642 0.05447132356064935 0.5403034015763207 chr9 141213431 7876398 0.05577655003651884 0.45232085978654285 chr10 135534747 2289084 0.01688927784695684 0.23316030856033645 chr11 135006516 7319662 0.05421710163974604 0.36095079841503636 chr12 133851895 5153991 0.038505177681645825 0.2407623737127299 chr13 115169878 3817886 0.033150039457365756 0.21471902845323998 chr14 107349540 6947567 0.0647191129091005 0.3238357403437395 chr15 102531392 7324329 0.07143499036860827 0.32237348184560954 chr16 90354753 3773821 0.04176671259341498 0.2689212522766477 chr17 81195210 7199642 0.08867077257389937 0.3806839425069839 chr18 78077248 4621996 0.05919773196924154 0.7649381104800325 chr19 59128983 3138648 0.05308137973555202 0.4630712484421767 chr20 63025520 4212957 0.06684525569959597 0.3123661706622357 chr21 48129895 3146584 0.06537691387026712 0.3289407547122485 chr22 51304566 1776284 0.03462233751280539 0.21692748227263517 chrMT 16571 52128 3.145736527668819 2.6035188082031095 chrX 155270560 5980537 0.03851687660558447 0.25689347293514947 chrY 59373566 297597 0.005012281054501595 0.13745291215071762