BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716767.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 = 1,297,960 number of mapped reads = 1,153,860 (88.9%) number of supplementary alignments = 5,140 (0.4%) number of secondary alignments = 0 number of mapped bases = 65,965,885 bp number of sequenced bases = 65,946,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,670 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9096 >>>>>>> ACTG content number of A's = 16,433,920 bp (24.92%) number of C's = 13,950,153 bp (21.15%) number of T's = 19,625,315 bp (29.76%) number of G's = 15,936,350 bp (24.17%) number of N's = 539 bp (0%) GC percentage = 45.32% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 334,118 number of insertions = 4,583 mapped reads with insertion percentage = 0.4% number of deletions = 12,147 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.1939X There is a 1.97% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5566809 0.02233418307110256 0.23023240343934975 chr2 243199373 5125561 0.021075551868301897 0.2794592869256038 chr3 198022430 3764902 0.019012502775569415 0.14929421099222778 chr4 191154276 3977706 0.020808877955730377 0.16687046440705317 chr5 180915260 3743474 0.020691864246277513 0.15215331821950748 chr6 171115067 3495357 0.02042693879201181 0.17496328980397421 chr7 159138663 3737015 0.0234827598118001 0.2642367782793638 chr8 146364022 3342341 0.02283581001894031 0.18091126083480621 chr9 141213431 2212761 0.015669621397415096 0.15051120272491525 chr10 135534747 2928068 0.02160381794935582 0.22950518641064177 chr11 135006516 2365864 0.01752407268994335 0.16769581826365473 chr12 133851895 3277621 0.02448692265432626 0.16787516528270138 chr13 115169878 1971538 0.017118521216111734 0.13932373324244224 chr14 107349540 2206874 0.020557833782985934 0.15717696594734032 chr15 102531392 2462017 0.024012323952453507 0.16947379334887894 chr16 90354753 2322274 0.025701735912000114 0.1823712829598051 chr17 81195210 2996516 0.03690508344026698 0.21349363430007506 chr18 78077248 1186127 0.015191711162770492 0.21266269438794602 chr19 59128983 1880987 0.03181159060354547 0.24103814815942298 chr20 63025520 2168525 0.034407094142182404 0.20663549492389624 chr21 48129895 834660 0.017341820504698794 0.1483334746146801 chr22 51304566 643294 0.012538728034459936 0.12019924821718889 chrMT 16571 4620 0.278800313801219 0.564338615719393 chrX 155270560 3539313 0.022794488536654986 0.1683492294822978 chrY 59373566 211661 0.0035649029401400617 0.10783669646439625