BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013312.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 = 1,396,288 number of mapped reads = 1,267,175 (90.75%) number of supplementary alignments = 11,104 (0.8%) number of secondary alignments = 0 number of mapped bases = 82,517,856 bp number of sequenced bases = 82,482,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,894 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6321 >>>>>>> ACTG content number of A's = 22,519,432 bp (27.3%) number of C's = 15,064,199 bp (18.26%) number of T's = 26,336,917 bp (31.93%) number of G's = 18,552,781 bp (22.49%) number of N's = 9,656 bp (0.01%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 578,611 number of insertions = 5,537 mapped reads with insertion percentage = 0.43% number of deletions = 20,040 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 0.2457X There is a 2.23% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 6207145 0.024903227823853645 0.31111365633893123 chr2 243199373 8061272 0.033146763088077534 0.33184379501584144 chr3 198022430 5394112 0.02723990408561293 0.19140957107712625 chr4 191154276 5343833 0.02795560273001688 0.19652246911808627 chr5 180915260 4749429 0.026252229911396086 0.18804701253659065 chr6 171115067 4604470 0.02690861816393994 0.21797422943556466 chr7 159138663 4976573 0.03127192918542994 0.35906711901040567 chr8 146364022 4506054 0.030786623231766615 0.3012636233846221 chr9 141213431 3048884 0.021590609182210153 0.2016811645071905 chr10 135534747 3770113 0.027816579020876468 0.2463492238068652 chr11 135006516 3518030 0.0260582237378824 0.20226944965477128 chr12 133851895 3984981 0.02977156953960196 0.20331637082347634 chr13 115169878 2239290 0.019443365217422563 0.1696215862363441 chr14 107349540 2668663 0.024859566235682053 0.18936648782614035 chr15 102531392 2315638 0.02258467338471324 0.17706661886758063 chr16 90354753 2496639 0.027631518178130594 0.1996772456534051 chr17 81195210 2090492 0.025746494158953467 0.1926006615832857 chr18 78077248 2021041 0.025885146464178655 0.3354505169188639 chr19 59128983 1590445 0.02689789202022974 0.27866810650228313 chr20 63025520 1783070 0.028291238215884612 0.1977461522917915 chr21 48129895 1322003 0.027467398380985455 0.19726350095316822 chr22 51304566 839192 0.01635706264428784 0.1460543965550592 chrMT 16571 211959 12.790960111037354 12.069282284260774 chrX 155270560 4592412 0.029576836716503116 0.2062566737004222 chrY 59373566 182116 0.003067290922024121 0.07635524302386576