BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068084.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 = 2,892,466 number of mapped reads = 2,503,801 (86.56%) number of supplementary alignments = 28,609 (0.99%) number of secondary alignments = 0 number of mapped bases = 166,793,624 bp number of sequenced bases = 166,728,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,218 duplication rate = 6.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1769 >>>>>>> ACTG content number of A's = 46,982,946 bp (28.18%) number of C's = 30,250,534 bp (18.14%) number of T's = 53,560,928 bp (32.12%) number of G's = 35,930,378 bp (21.55%) number of N's = 3,752 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 1,173,762 number of insertions = 11,854 mapped reads with insertion percentage = 0.47% number of deletions = 40,747 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.0539X std coverageData = 0.4407X There is a 3.64% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 16791481 0.06736786023895203 0.40226229063848995 chr2 243199373 26566500 0.1092375349174934 0.6079222156805706 chr3 198022430 3575096 0.01805399519640275 0.18888955502632762 chr4 191154276 3833169 0.02005275048097799 0.195378278543274 chr5 180915260 7199557 0.03979518919520664 0.26938858344781047 chr6 171115067 5044195 0.029478380182617114 0.24898193139621325 chr7 159138663 26986934 0.16958125380254074 1.1595618076793506 chr8 146364022 6207338 0.042410272109084296 0.3896526252053122 chr9 141213431 6886073 0.048763583968156686 0.31936229104108244 chr10 135534747 5974374 0.0440800173552543 0.41658017890775473 chr11 135006516 6716785 0.049751561620922057 0.45427471141800657 chr12 133851895 3207521 0.023963209486126437 0.21222405334679395 chr13 115169878 1545210 0.013416789414329326 0.15850000374071163 chr14 107349540 3790393 0.03530888907395411 0.2569486943860629 chr15 102531392 2667158 0.026013086801747506 0.22384260719014962 chr16 90354753 3697892 0.04092636941855178 0.2784215348595065 chr17 81195210 2745636 0.03381524599788584 0.26999952788788956 chr18 78077248 1854283 0.023749338603737673 0.3775548908966048 chr19 59128983 529122 0.008948606472734362 0.20432350843825262 chr20 63025520 464205 0.007365349782120004 0.12605755207929398 chr21 48129895 3216238 0.06682412251262962 0.3605418115184423 chr22 51304566 2203426 0.04294795126032252 0.27631525719388667 chrMT 16571 52315 3.1570213022750586 2.948408760052409 chrX 155270560 24658172 0.15880777399141216 0.6465285292302924 chrY 59373566 380551 0.006409434797970531 0.10124670789271875