BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,301,594 number of mapped reads = 3,195,548 (96.79%) number of supplementary alignments = 28,546 (0.86%) number of secondary alignments = 0 number of mapped bases = 248,250,561 bp number of sequenced bases = 248,100,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 579,358 duplication rate = 16.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.153 >>>>>>> ACTG content number of A's = 72,590,377 bp (29.26%) number of C's = 49,448,597 bp (19.93%) number of T's = 73,473,178 bp (29.61%) number of G's = 52,568,614 bp (21.19%) number of N's = 19,556 bp (0.01%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,402,285 number of insertions = 30,112 mapped reads with insertion percentage = 0.92% number of deletions = 84,903 mapped reads with deletion percentage = 2.62% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 0.0802X std coverageData = 0.8022X There is a 5.71% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% 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 0.01% 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 20883665 0.08378580930396157 1.6753328496656084 chr2 243199373 21806229 0.08966400172421497 1.0577476741732088 chr3 198022430 16836757 0.08502449444742194 0.38470857683539583 chr4 191154276 16124325 0.08435241595118699 0.44210585493813304 chr5 180915260 15222555 0.08414190710059505 0.3969520644425175 chr6 171115067 14746543 0.08617910309441074 0.4654669241684905 chr7 159138663 13286203 0.08348821555702023 1.0984699178307937 chr8 146364022 12164166 0.08310898972153143 0.5370632405052571 chr9 141213431 10338190 0.07320967932575762 0.7785719005275389 chr10 135534747 13932811 0.10279881217471118 0.8100480624731398 chr11 135006516 11261288 0.0834129220844422 0.5213990722142794 chr12 133851895 11520365 0.08606800075561127 0.3968987153479928 chr13 115169878 7583054 0.0658423376987514 0.33500689062844985 chr14 107349540 7534870 0.07019005391173544 0.5056343309335992 chr15 102531392 7296124 0.07115990388582649 0.3501082094412516 chr16 90354753 6831059 0.07560265257988144 0.6423682717537023 chr17 81195210 6699137 0.08250655426594747 0.46592277846666946 chr18 78077248 6261753 0.08019945836205702 0.9975157871485859 chr19 59128983 4998278 0.08453177691217859 1.6032227367039953 chr20 63025520 5046977 0.08007830796160031 0.4069445156645333 chr21 48129895 2883669 0.059914300664898605 0.3528365393317871 chr22 51304566 2899277 0.056511091040123015 0.33510611946340546 chrMT 16571 249548 15.059320499668095 9.04845666750148 chrX 155270560 11208173 0.07218479150200785 0.4144855701694986 chrY 59373566 635545 0.010704174312184652 0.7088577683619367