BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716435.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 = 1,598,019 number of mapped reads = 1,389,245 (86.94%) number of supplementary alignments = 7,324 (0.46%) number of secondary alignments = 0 number of mapped bases = 79,030,831 bp number of sequenced bases = 79,006,995 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,513 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3786 >>>>>>> ACTG content number of A's = 20,489,264 bp (25.93%) number of C's = 15,616,584 bp (19.77%) number of T's = 24,609,112 bp (31.15%) number of G's = 18,290,864 bp (23.15%) number of N's = 1,171 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 394,048 number of insertions = 6,602 mapped reads with insertion percentage = 0.47% number of deletions = 15,270 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.25% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.251X There is a 2.32% of reference with a coverageData >= 1X There is a 0.17% 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 6311779 0.02532302216410526 0.2769321813116543 chr2 243199373 7600237 0.03125105507570532 0.30105122004954926 chr3 198022430 6029319 0.03044765686392193 0.2008339596356785 chr4 191154276 4494720 0.02351357287974034 0.1683992214885201 chr5 180915260 4006602 0.022146291031502816 0.16098252732961757 chr6 171115067 4437984 0.025935670527481955 0.1900357520539926 chr7 159138663 4887633 0.030713045515532576 0.6071027662346067 chr8 146364022 6431374 0.043940948821425525 0.2606403134112289 chr9 141213431 3167900 0.022433418532264115 0.1889507177081057 chr10 135534747 3648188 0.026916994208134686 0.30759807275081297 chr11 135006516 2778643 0.02058154733805589 0.186919626816971 chr12 133851895 3634689 0.02715455765493645 0.1851813424089584 chr13 115169878 2077724 0.018040515767499554 0.14460324743076863 chr14 107349540 2494091 0.023233364577062928 0.17001436670536443 chr15 102531392 1815058 0.017702461310580862 0.14619670997337894 chr16 90354753 2285717 0.02529714181167647 0.18056849312343512 chr17 81195210 3119097 0.038414790724723785 0.21864942475476049 chr18 78077248 1817569 0.023279111989193062 0.27256575672246025 chr19 59128983 1469959 0.024860211108315527 0.2728841546459217 chr20 63025520 1667356 0.02645525177737526 0.17729943886231553 chr21 48129895 783473 0.016278302705626097 0.13847419350528858 chr22 51304566 1058527 0.020632218192821277 0.15521442353133819 chrMT 16571 51097 3.0835194013638283 2.7888129061719105 chrX 155270560 2800729 0.018037733618014903 0.16469177384139125 chrY 59373566 161366 0.0027178087972684678 0.06931443185075035