BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238538.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 = 7,726,988 number of mapped reads = 6,868,696 (88.89%) number of supplementary alignments = 71,095 (0.92%) number of secondary alignments = 0 number of mapped bases = 424,957,541 bp number of sequenced bases = 424,718,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,023,675 duplication rate = 21.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.275 >>>>>>> ACTG content number of A's = 104,609,737 bp (24.63%) number of C's = 75,796,760 bp (17.85%) number of T's = 142,003,057 bp (33.43%) number of G's = 102,279,746 bp (24.08%) number of N's = 28,915 bp (0.01%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 2,624,741 number of insertions = 27,534 mapped reads with insertion percentage = 0.4% number of deletions = 143,215 mapped reads with deletion percentage = 2.06% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.1373X std coverageData = 2.341X There is a 2.99% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 1.37% of reference with a coverageData >= 3X There is a 1.14% of reference with a coverageData >= 4X There is a 0.95% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.57% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 21043134 0.08442560309609018 1.731190312220839 chr2 243199373 67275889 0.2766285462421813 6.143597889933206 chr3 198022430 17964192 0.09071796563651906 1.0167628299837044 chr4 191154276 5866052 0.03068752696905404 0.5411562172028243 chr5 180915260 19188587 0.10606394949768196 1.1157791801623063 chr6 171115067 103481786 0.6047497033092942 3.795333783409423 chr7 159138663 6216045 0.03906055814984445 0.9946638100487185 chr8 146364022 19168879 0.13096715120331962 1.4241948120783834 chr9 141213431 27238576 0.19288941432206969 1.7303861666182245 chr10 135534747 14611830 0.1078087377844148 1.2367737569496098 chr11 135006516 7321935 0.05423393786415465 0.7791617469932053 chr12 133851895 13930605 0.1040747686089913 1.100698359652298 chr13 115169878 10446551 0.09070558362491275 1.4140119677525278 chr14 107349540 3753533 0.034965524770762875 0.7612629662852456 chr15 102531392 4031981 0.03932435638833422 1.2072162980993708 chr16 90354753 17844816 0.1974972583899377 1.65679720525116 chr17 81195210 3788912 0.04666423056236938 0.7007877784457026 chr18 78077248 5338887 0.06837954893082297 3.9641729119551496 chr19 59128983 8860975 0.14985840361908473 1.522175078669672 chr20 63025520 26365734 0.4183342557110199 2.273514802324241 chr21 48129895 1433720 0.029788554494041594 0.6088314134762944 chr22 51304566 3203020 0.06243148027019661 0.8138592513749974 chrMT 16571 341562 20.61203306982077 19.57554935190595 chrX 155270560 15255933 0.09825386731393253 1.0850448988942052 chrY 59373566 984407 0.016579886746233164 0.7492100649361996