BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 929,591 number of mapped reads = 851,485 (91.6%) number of supplementary alignments = 2,596 (0.28%) number of secondary alignments = 0 number of mapped bases = 49,459,231 bp number of sequenced bases = 49,443,162 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,441 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.404 >>>>>>> ACTG content number of A's = 12,804,925 bp (25.9%) number of C's = 9,986,990 bp (20.2%) number of T's = 14,950,323 bp (30.24%) number of G's = 11,700,361 bp (23.66%) number of N's = 563 bp (0%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 244,420 number of insertions = 2,725 mapped reads with insertion percentage = 0.32% number of deletions = 9,320 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 0.1698X There is a 1.5% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5247449 0.021052902411825888 0.2957123545623598 chr2 243199373 4774893 0.019633656703547504 0.19592945995821473 chr3 198022430 2723564 0.013753815666235385 0.12246741372784056 chr4 191154276 3225297 0.016872743144914007 0.1395826295474881 chr5 180915260 2156521 0.011920061359113653 0.11581983309579483 chr6 171115067 3353079 0.019595463209560616 0.1925253289430078 chr7 159138663 3103210 0.01950003815226222 0.20797102827576894 chr8 146364022 2986472 0.020404413319551985 0.17818068111377902 chr9 141213431 1361528 0.009641632459167429 0.1296088086155874 chr10 135534747 2513314 0.018543687546043082 0.16844015218914146 chr11 135006516 2069361 0.015327860175282206 0.15579551158498953 chr12 133851895 2708229 0.02023302695863962 0.14874736551443482 chr13 115169878 978056 0.008492289971862261 0.09732271304440622 chr14 107349540 1141451 0.010633031124306634 0.11032208550087184 chr15 102531392 1368815 0.013350204003862543 0.13007650733202075 chr16 90354753 1561714 0.01728424845564018 0.14188165508975653 chr17 81195210 1238471 0.015253005688389746 0.15163603662727554 chr18 78077248 981808 0.012574828457068568 0.1914730204202451 chr19 59128983 1198319 0.020266186550172864 0.1886290739058193 chr20 63025520 1174042 0.018628041466377428 0.1425337054760108 chr21 48129895 715039 0.014856442134353295 0.12931880623167832 chr22 51304566 644945 0.012570908406086117 0.11661728627426328 chrMT 16571 16886 1.0190091123046285 1.2302691826265413 chrX 155270560 2090821 0.013465662775995656 0.13466095257533792 chrY 59373566 125947 0.0021212638634506135 0.061702126478990794