BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926902.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 21,190,182 number of mapped reads = 19,082,400 (90.05%) number of supplementary alignments = 586,181 (2.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,585,590 number of mapped paired reads (second in pair) = 9,496,810 number of mapped paired reads (both in pair) = 18,589,284 number of mapped paired reads (singletons) = 493,116 number of mapped bases = 1,721,887,895 bp number of sequenced bases = 1,720,549,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,358,529 duplication rate = 5.75% >>>>>>> Insert size mean insert size = 419,596.0523 std insert size = 6,372,620.3242 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.4152 >>>>>>> ACTG content number of A's = 489,731,194 bp (28.46%) number of C's = 331,057,769 bp (19.24%) number of T's = 497,390,073 bp (28.91%) number of G's = 402,229,455 bp (23.38%) number of N's = 140,555 bp (0.01%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 18,664,437 number of insertions = 295,575 mapped reads with insertion percentage = 1.52% number of deletions = 915,263 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.07% >>>>>>> Coverage mean coverageData = 0.5562X std coverageData = 1.9644X There is a 27.78% of reference with a coverageData >= 1X There is a 12.58% of reference with a coverageData >= 2X There is a 6.25% of reference with a coverageData >= 3X There is a 3.38% of reference with a coverageData >= 4X There is a 1.92% of reference with a coverageData >= 5X There is a 1.14% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 144691333 0.5805054062433008 1.7600941151150105 chr2 243199373 149838974 0.6161157907261545 2.574669909155549 chr3 198022430 118083410 0.5963133065279524 1.2974710186183094 chr4 191154276 104923363 0.548893622447661 1.3396533753875182 chr5 180915260 105976741 0.5857811054744636 1.263685556587753 chr6 171115067 100368933 0.5865581258253547 1.4226668780116383 chr7 159138663 90370450 0.567872371781834 1.4875320466305202 chr8 146364022 71095238 0.4857425822856931 1.1836647356931116 chr9 141213431 69244810 0.4903556942823661 1.8812794112632463 chr10 135534747 86189131 0.6359190754235148 5.607865657338295 chr11 135006516 83251419 0.6166474142625827 1.56803878543921 chr12 133851895 79115594 0.5910681653031509 1.3887328895128903 chr13 115169878 52901860 0.4593376403507174 1.1236196040406752 chr14 107349540 52510336 0.48915287387351636 1.1843373152117609 chr15 102531392 52379427 0.5108623415548674 1.2808750402576723 chr16 90354753 54236437 0.6002610288802406 2.5820981178387363 chr17 81195210 45429085 0.5595044954006523 1.3553082463379489 chr18 78077248 46217684 0.5919481690748116 1.9151257827874264 chr19 59128983 28772464 0.4866050884047845 1.3715277652315736 chr20 63025520 39252413 0.6228018904088376 1.4002584763567134 chr21 48129895 22050858 0.4581530460434206 1.5416370180277796 chr22 51304566 21934613 0.4275372488288859 1.1870984655196115 chrMT 16571 112377 6.781546074467443 4.943105491872438 chrX 155270560 100122024 0.6448229722363338 1.3973572777449161 chrY 59373566 2818921 0.04747771087220869 1.216852538027287