BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716786.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,668,797 number of mapped reads = 2,217,434 (83.09%) number of supplementary alignments = 46,908 (1.76%) number of secondary alignments = 0 number of mapped bases = 164,174,448 bp number of sequenced bases = 164,116,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,994 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1841 >>>>>>> ACTG content number of A's = 43,429,540 bp (26.46%) number of C's = 32,260,712 bp (19.66%) number of T's = 49,242,360 bp (30%) number of G's = 39,164,368 bp (23.86%) number of N's = 20,005 bp (0.01%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,214,650 number of insertions = 13,827 mapped reads with insertion percentage = 0.62% number of deletions = 33,957 mapped reads with deletion percentage = 1.51% homopolymer indels = 40.49% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.4078X There is a 4.44% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 12972607 0.052046438030740154 0.4555430333763942 chr2 243199373 13864215 0.057007609966165496 0.6027397414054081 chr3 198022430 10982312 0.05545993956341209 0.27127511107015134 chr4 191154276 10510685 0.05498535120396679 0.2991342252786023 chr5 180915260 9735126 0.053810419309017934 0.27094161707305986 chr6 171115067 9658614 0.05644514050887173 0.32092915185219084 chr7 159138663 9041093 0.05681267411427228 0.5331356502808826 chr8 146364022 8416007 0.05750051744273603 0.5297242150364209 chr9 141213431 6976465 0.04940369305239811 0.4460693942160667 chr10 135534747 7791650 0.05748821001598948 0.3851224015907759 chr11 135006516 7485668 0.05544671636441607 0.45506532531467314 chr12 133851895 7440376 0.05558663177686054 0.27722450486840844 chr13 115169878 5299150 0.04601159688647061 0.24662965432308218 chr14 107349540 4974185 0.04633634200947671 0.30299052245332186 chr15 102531392 4772531 0.04654702239875959 0.2517955490559101 chr16 90354753 4849265 0.05366917443734255 0.2974495014288595 chr17 81195210 4413989 0.054362677305717914 0.2992312016809891 chr18 78077248 4514322 0.05781866184627819 0.8325147964352704 chr19 59128983 3261429 0.055157874100422125 0.44468058290620854 chr20 63025520 3532667 0.056051374110043045 0.2906687605161127 chr21 48129895 2151334 0.04469849768008013 0.2720914452751232 chr22 51304566 1836210 0.03579038169819037 0.21908103848911495 chrMT 16571 19220 1.1598575825236859 1.429102086867875 chrX 155270560 9263542 0.059660646551413225 0.36567528822189915 chrY 59373566 411786 0.006935510661428016 0.20526612235879288