BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238659.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 = 3,913,485 number of mapped reads = 3,383,205 (86.45%) number of supplementary alignments = 28,968 (0.74%) number of secondary alignments = 0 number of mapped bases = 207,467,989 bp number of sequenced bases = 207,371,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,491,908 duplication rate = 22.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3195 >>>>>>> ACTG content number of A's = 52,371,217 bp (25.25%) number of C's = 36,027,516 bp (17.37%) number of T's = 69,393,735 bp (33.46%) number of G's = 49,574,613 bp (23.91%) number of N's = 4,823 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,101,135 number of insertions = 14,013 mapped reads with insertion percentage = 0.41% number of deletions = 56,388 mapped reads with deletion percentage = 1.65% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 1.0446X There is a 1.46% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 11221394 0.0450205257462528 0.8230078783156075 chr2 243199373 11033060 0.04536631761793235 1.5972244691297237 chr3 198022430 11124119 0.05617605540948063 0.7701700782616969 chr4 191154276 8293405 0.04338592457120865 0.6660724049571594 chr5 180915260 16717411 0.0924046484525407 0.9859061790077511 chr6 171115067 10444509 0.0610379271861548 0.9678820330740587 chr7 159138663 12048779 0.0757124558725242 1.2877345991265292 chr8 146364022 5580996 0.03813092810472235 0.869162310857341 chr9 141213431 11090761 0.07853899534527987 0.9236158883045228 chr10 135534747 8957270 0.06608836625489108 0.958952929551102 chr11 135006516 6928045 0.05131637498148608 0.7206264304492647 chr12 133851895 8997881 0.06722266427382294 0.8448391502401928 chr13 115169878 6649819 0.0577392206667094 0.8930698931311997 chr14 107349540 4354330 0.040562167290143954 0.7334311656002198 chr15 102531392 4533400 0.04421475132220969 0.7718413992690065 chr16 90354753 4906417 0.05430170342007354 0.7816491597766224 chr17 81195210 7148971 0.0880467086666812 0.9602962467182558 chr18 78077248 1734893 0.02222021196238884 1.9569615189756668 chr19 59128983 4068458 0.06880649376296562 0.9169716253891663 chr20 63025520 2394567 0.037993609572757193 0.6260830491468142 chr21 48129895 3233604 0.06718493776061635 0.8412332989708029 chr22 51304566 1822786 0.03552872857359324 0.5730416604583509 chrMT 16571 25300 1.5267636231971518 4.089052955838372 chrX 155270560 43119807 0.2777075512576241 1.7585606520085846 chrY 59373566 1038007 0.017482645391385117 0.4315689401486138