BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237825.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 = 3,902,620 number of mapped reads = 3,629,682 (93.01%) number of supplementary alignments = 38,598 (0.99%) number of secondary alignments = 0 number of mapped bases = 260,725,376 bp number of sequenced bases = 260,518,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,835 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9093 >>>>>>> ACTG content number of A's = 78,768,860 bp (30.24%) number of C's = 50,663,175 bp (19.45%) number of T's = 78,608,624 bp (30.17%) number of G's = 52,020,020 bp (19.97%) number of N's = 457,387 bp (0.18%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 2,487,735 number of insertions = 19,116 mapped reads with insertion percentage = 0.52% number of deletions = 118,003 mapped reads with deletion percentage = 3.2% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.0842X std coverageData = 0.9143X There is a 2.72% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 19002681 0.0762392523788336 1.2000536181445975 chr2 243199373 13332605 0.05482170794905791 0.7401131838627775 chr3 198022430 23030050 0.11630020902177597 0.8524274642563976 chr4 191154276 26275825 0.13745873516321444 0.9517425299321622 chr5 180915260 8191884 0.04528022677578442 0.5213309509385159 chr6 171115067 18635221 0.10890461796680943 0.9271200309344653 chr7 159138663 12727339 0.07997641025801505 0.9008526071504551 chr8 146364022 6437957 0.043985925721554714 1.256391079222604 chr9 141213431 5581866 0.03952786898860917 0.662689080924207 chr10 135534747 12318668 0.09088937171218536 1.0236457297314465 chr11 135006516 18255952 0.1352227473228033 1.0971165663287759 chr12 133851895 13040725 0.09742652504097907 0.7945891610769201 chr13 115169878 11988466 0.1040937631278901 0.8148046888989682 chr14 107349540 11627614 0.10831545249285651 0.8640702632022585 chr15 102531392 8974382 0.08752813967453012 0.7437538388073534 chr16 90354753 4195683 0.046435664541078434 0.5842467273454458 chr17 81195210 7550332 0.09298986972261049 0.9847635821722855 chr18 78077248 2433445 0.031167146157610473 1.42148352756893 chr19 59128983 2239159 0.037869059916014455 0.8613990611981163 chr20 63025520 4985495 0.0791027983585062 0.7425919167710824 chr21 48129895 3631478 0.07545160861040731 0.6960623828386023 chr22 51304566 1314619 0.02562382069463369 0.3722486445983561 chrMT 16571 16811 1.0144831331844788 2.4106829552426654 chrX 155270560 24134409 0.15543454599506823 1.0449485234742077 chrY 59373566 802710 0.013519652836752301 0.35424711376165