BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714198.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 102,590 number of mapped reads = 24,141 (23.53%) number of supplementary alignments = 1,037 (1.01%) number of secondary alignments = 0 number of mapped bases = 2,640,627 bp number of sequenced bases = 2,610,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,242 duplication rate = 50.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.0243 >>>>>>> ACTG content number of A's = 379,483 bp (14.53%) number of C's = 310,284 bp (11.88%) number of T's = 345,366 bp (13.23%) number of G's = 1,575,760 bp (60.35%) number of N's = 58 bp (0%) GC percentage = 72.24% >>>>>>> Mismatches and indels general error rate = 0.0344 number of mismatches = 77,473 number of insertions = 2,007 mapped reads with insertion percentage = 5.87% number of deletions = 4,219 mapped reads with deletion percentage = 16.93% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 1.5752X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 46133 1.8508680064632617E-4 0.18557586120624767 chr2 243199373 1344594 0.0055287724775507545 5.587686679422398 chr3 198022430 31196 1.5753770923829184E-4 0.03849275044906081 chr4 191154276 16736 8.755231821233233E-5 0.026826140130315028 chr5 180915260 51100 2.8245267977947244E-4 0.11005371012866404 chr6 171115067 38550 2.2528699942010367E-4 0.06109219730053473 chr7 159138663 53946 3.3898738988400324E-4 0.15553287531948257 chr8 146364022 82091 5.608687085682846E-4 0.2597938515870228 chr9 141213431 16401 1.1614334333396375E-4 0.03210765331750386 chr10 135534747 31790 2.3455239858159767E-4 0.2520855372589342 chr11 135006516 22555 1.6706601035464095E-4 0.04308821523901974 chr12 133851895 27644 2.0652677349095432E-4 0.044763740911484835 chr13 115169878 9797 8.506564537647596E-5 0.022573090806802705 chr14 107349540 19287 1.7966541822163375E-4 0.06965976778638872 chr15 102531392 18217 1.7767241470787796E-4 0.04216114061363113 chr16 90354753 21376 2.3657858928572358E-4 0.06842547538148794 chr17 81195210 34771 4.2823954762848695E-4 0.10697802413360313 chr18 78077248 11728 1.502102123271558E-4 0.04563980134538487 chr19 59128983 7543 1.2756857326634555E-4 0.038441114352114863 chr20 63025520 30988 4.916738489424601E-4 0.14675149982406485 chr21 48129895 3495 7.261599053976743E-5 0.026886662612638477 chr22 51304566 1840 3.5864254265400084E-5 0.010236440241917498 chrMT 16571 337 0.020336732846539134 0.371917684342628 chrX 155270560 711289 0.004580964994265494 0.5645847614442036 chrY 59373566 7223 1.2165346443904009E-4 0.02123701826996902