BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251063.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,438,006 number of mapped reads = 3,312,455 (96.35%) number of supplementary alignments = 28,740 (0.84%) number of secondary alignments = 0 number of mapped bases = 256,999,242 bp number of sequenced bases = 256,845,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 635,500 duplication rate = 16.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0666 >>>>>>> ACTG content number of A's = 74,793,324 bp (29.12%) number of C's = 51,325,105 bp (19.98%) number of T's = 75,929,678 bp (29.56%) number of G's = 54,776,210 bp (21.33%) number of N's = 21,476 bp (0.01%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,447,009 number of insertions = 31,322 mapped reads with insertion percentage = 0.93% number of deletions = 85,870 mapped reads with deletion percentage = 2.55% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.083X std coverageData = 0.8154X There is a 5.78% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 20936732 0.08399871549367173 1.6659516437433557 chr2 243199373 22741376 0.09350918844679752 1.065240580006159 chr3 198022430 17127531 0.08649288365969451 0.39527445068887507 chr4 191154276 15745744 0.08237191617936918 0.4482431084078683 chr5 180915260 15818810 0.08743767662274592 0.41393400374985406 chr6 171115067 15014008 0.08774217410089317 0.47200137614964327 chr7 159138663 14046696 0.08826702282901547 1.1333612583454187 chr8 146364022 12287035 0.08394846514944772 0.5476060617384637 chr9 141213431 11225330 0.07949194294415239 0.8430653734080045 chr10 135534747 15300302 0.11288840934642391 0.828723564776434 chr11 135006516 11839212 0.08769363398726622 0.5419796177265386 chr12 133851895 11607793 0.08672117043991047 0.4064927118629066 chr13 115169878 7465353 0.06482036040708491 0.336711808586329 chr14 107349540 7771214 0.07239168421215406 0.5644737500108711 chr15 102531392 7689291 0.07499450509752174 0.36591045207004586 chr16 90354753 7237644 0.08010252653781257 0.6669621061435149 chr17 81195210 7330734 0.09028530131272522 0.4916931430567016 chr18 78077248 6357742 0.08142886900931755 1.0306219013490687 chr19 59128983 5403528 0.09138543783173135 1.5953970905283898 chr20 63025520 5179974 0.08218851665166745 0.4379698508072288 chr21 48129895 3059342 0.06356427746206386 0.37474911813136114 chr22 51304566 3225389 0.06286748434827419 0.3488989403715727 chrMT 16571 277920 16.771468227626578 10.149254984417064 chrX 155270560 11639910 0.07496533792368625 0.43785525025948036 chrY 59373566 670632 0.011295127532006415 0.742270284364707