BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237261.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 = 2,903,370 number of mapped reads = 2,617,993 (90.17%) number of supplementary alignments = 24,824 (0.86%) number of secondary alignments = 0 number of mapped bases = 162,087,467 bp number of sequenced bases = 161,989,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 343,639 duplication rate = 11.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6954 >>>>>>> ACTG content number of A's = 42,467,335 bp (26.22%) number of C's = 27,953,873 bp (17.26%) number of T's = 54,138,906 bp (33.42%) number of G's = 37,411,614 bp (23.1%) number of N's = 17,753 bp (0.01%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,000,121 number of insertions = 11,309 mapped reads with insertion percentage = 0.43% number of deletions = 56,296 mapped reads with deletion percentage = 2.12% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.0524X std coverageData = 0.6034X There is a 3.82% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 11358767 0.045571669809400396 0.6239466769183334 chr2 243199373 14459725 0.05945625937119501 1.2034336477070813 chr3 198022430 5702442 0.02879694992127912 0.22633433247381296 chr4 191154276 7698270 0.04027254927846866 0.3496005729952444 chr5 180915260 7168887 0.03962566231284193 0.26736600282227857 chr6 171115067 15268254 0.0892279929972502 0.5735073407509881 chr7 159138663 16156438 0.10152427886113383 1.0525333910903198 chr8 146364022 7699189 0.05260301606087321 0.8264106287619558 chr9 141213431 6107556 0.043250531884605224 0.4226509915115333 chr10 135534747 6857010 0.05059226620314568 0.4807425664483101 chr11 135006516 7624357 0.05647399270713719 0.40894869728387095 chr12 133851895 3887618 0.029044176027541484 0.2569258518478719 chr13 115169878 5912310 0.05133555841745356 0.34577021311616385 chr14 107349540 5858758 0.05457646115670361 0.3303615267594557 chr15 102531392 5626959 0.054880353131263444 0.3409391472416276 chr16 90354753 2467473 0.02730872386978912 0.2777143804159306 chr17 81195210 4496585 0.055379929431797766 0.3754011388643535 chr18 78077248 6625251 0.08485507839620576 1.1333576746701028 chr19 59128983 2201894 0.03723882753065447 0.4152409957402538 chr20 63025520 3104019 0.04925019262038616 0.30026302004400773 chr21 48129895 3208196 0.06665703301451208 0.38455846213501615 chr22 51304566 1110040 0.02163628087215473 0.18438223347053762 chrMT 16571 14444 0.8716432321525557 1.2536575286389362 chrX 155270560 10961170 0.07059400056263081 0.39383120029035495 chrY 59373566 511855 0.008620923998400231 0.28197284777544