BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238661.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 = 2,931,813 number of mapped reads = 2,654,627 (90.55%) number of supplementary alignments = 21,591 (0.74%) number of secondary alignments = 0 number of mapped bases = 163,241,224 bp number of sequenced bases = 163,171,867 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 938,626 duplication rate = 21.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.641 >>>>>>> ACTG content number of A's = 39,594,370 bp (24.27%) number of C's = 28,688,910 bp (17.58%) number of T's = 54,900,985 bp (33.65%) number of G's = 39,979,696 bp (24.5%) number of N's = 7,906 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 920,348 number of insertions = 10,152 mapped reads with insertion percentage = 0.38% number of deletions = 41,589 mapped reads with deletion percentage = 1.55% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.8183X There is a 1.91% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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% 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 5281250 0.0211885129064533 0.6170967158597548 chr2 243199373 3344861 0.013753575754490124 1.8510722561206594 chr3 198022430 16822901 0.08495452257605363 0.6878980495205623 chr4 191154276 6488184 0.03394213373495239 0.41647156214134484 chr5 180915260 31941522 0.17655515626487228 1.0155730072774722 chr6 171115067 7134080 0.041691711461036916 0.7310952741939811 chr7 159138663 2960436 0.018602870881226394 0.4056624530027216 chr8 146364022 3261883 0.0222860984238326 0.582801333278333 chr9 141213431 2581138 0.0182782755274886 0.4877564381139915 chr10 135534747 9896665 0.07301939332206818 0.6707231479446517 chr11 135006516 7162869 0.053055728065747584 0.5390298217441665 chr12 133851895 2875210 0.02148053264393455 0.3286432127655551 chr13 115169878 3935687 0.034172885031622593 0.5499682638132466 chr14 107349540 1734062 0.016153418077059296 0.28591632008863105 chr15 102531392 944456 0.009211383768202425 0.4020717198543869 chr16 90354753 806486 0.00892577283676488 0.21349699872628214 chr17 81195210 6795258 0.08369038025765313 0.703749647641079 chr18 78077248 11450976 0.14666213645235038 1.4616983293341688 chr19 59128983 2617592 0.044269186906191166 0.651410791678872 chr20 63025520 11009547 0.17468395342077306 1.0500256461628772 chr21 48129895 736874 0.015310110275536649 0.2746927180120957 chr22 51304566 1430229 0.027877226366167875 0.40198637770386486 chrMT 16571 5468 0.32997405105304445 0.7915164010136236 chrX 155270560 21546611 0.13876816699830283 0.8960714691323302 chrY 59373566 476979 0.008033524548618151 0.2942892377463936