BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231732.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 = 4,059,657 number of mapped reads = 2,500,205 (61.59%) number of supplementary alignments = 29,521 (0.73%) number of secondary alignments = 0 number of mapped bases = 172,333,953 bp number of sequenced bases = 172,280,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,783 duplication rate = 12.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6005 >>>>>>> ACTG content number of A's = 41,867,331 bp (24.3%) number of C's = 29,466,102 bp (17.1%) number of T's = 45,333,026 bp (26.31%) number of G's = 55,577,671 bp (32.26%) number of N's = 35,933 bp (0.02%) GC percentage = 49.36% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,003,838 number of insertions = 10,254 mapped reads with insertion percentage = 0.41% number of deletions = 33,109 mapped reads with deletion percentage = 1.31% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.0557X std coverageData = 45.3344X There is a 1.38% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 13069413 0.052434826230583396 0.6238581526808187 chr2 243199373 31592326 0.12990299115614906 161.72909289021445 chr3 198022430 25315420 0.12784117435585454 0.9372040034082699 chr4 191154276 3509755 0.01836085006018908 0.3295965767817381 chr5 180915260 26499323 0.14647367502332306 1.0077717900576046 chr6 171115067 24160917 0.14119689997842214 1.2780935040876997 chr7 159138663 3713715 0.023336346617415026 0.42412439612927316 chr8 146364022 2920404 0.01995301823558798 0.38156227267893306 chr9 141213431 2243123 0.01588462927439246 0.34587239536428555 chr10 135534747 3600232 0.026563166123001653 0.45299960399063094 chr11 135006516 2467149 0.018274295738436804 0.4022089039307234 chr12 133851895 12302955 0.09191468675135306 0.7832160449122005 chr13 115169878 1544453 0.013410216515120386 0.28393561266791223 chr14 107349540 3322128 0.03094683032642711 0.5462778456234182 chr15 102531392 2022970 0.019730250029181308 0.3611988623360788 chr16 90354753 1446399 0.01600800126142783 0.3245609350597716 chr17 81195210 1414667 0.01742303517658246 0.32515825136899884 chr18 78077248 1271584 0.016286229760557134 0.3517165304773261 chr19 59128983 1735139 0.02934498298406384 0.4629622841539904 chr20 63025520 2358042 0.03741408242248537 0.5126679129349262 chr21 48129895 984140 0.02044758252641108 0.36354067886589375 chr22 51304566 2061797 0.04018739774545603 0.5302000289736738 chrMT 16571 70139 4.232635326775693 6.0775098558807965 chrX 155270560 2498157 0.01608905770675394 0.2947517089061455 chrY 59373566 209606 0.0035302915779052246 0.10553866105508034