BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6234065.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 = 5,289,275
number of mapped reads = 4,967,784 (93.92%)
number of supplementary alignments = 33,364 (0.63%)
number of secondary alignments = 0
number of mapped bases = 336,358,537 bp
number of sequenced bases = 336,242,387 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 517,560
duplication rate = 4.37%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0957
>>>>>>> ACTG content
number of A's = 87,986,280 bp (26.17%)
number of C's = 60,653,520 bp (18.04%)
number of T's = 97,181,854 bp (28.9%)
number of G's = 90,349,514 bp (26.87%)
number of N's = 71,219 bp (0.02%)
GC percentage = 44.91%
>>>>>>> Mismatches and indels
general error rate = 0.0064
number of mismatches = 2,122,870
number of insertions = 22,250
mapped reads with insertion percentage = 0.44%
number of deletions = 71,744
mapped reads with deletion percentage = 1.43%
homopolymer indels = 46.74%
>>>>>>> Coverage
mean coverageData = 0.1087X
std coverageData = 37.3352X
There is a 7.34% of reference with a coverageData >= 1X
There is a 1.89% of reference with a coverageData >= 2X
There is a 0.55% of reference with a coverageData >= 3X
There is a 0.18% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.03% of reference with a coverageData >= 6X
There is a 0.02% 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 31432937 0.1261097640354525 1.2737379897132717
chr2 243199373 43698918 0.17968351423340223 133.17833507124118
chr3 198022430 30303272 0.15302949266908805 0.5186070680037599
chr4 191154276 16769125 0.0877256075610885 0.4066784019174545
chr5 180915260 20553278 0.11360721035914825 0.4498381847294178
chr6 171115067 26351966 0.15400143577070277 0.6449570184231795
chr7 159138663 17065876 0.10723903090727864 1.3751258432930282
chr8 146364022 13347651 0.0911948907771884 0.9643700640875232
chr9 141213431 10983861 0.07778198519941067 0.6433434429898142
chr10 135534747 9018542 0.06654044220852089 0.5854538727537094
chr11 135006516 11080127 0.08207105351863164 0.7241406911276312
chr12 133851895 10199544 0.07620022114741072 0.37702406021685303
chr13 115169878 9800576 0.08509669516190684 0.38292887111787327
chr14 107349540 13356411 0.12441982518043393 0.6917762972223015
chr15 102531392 4024001 0.03924652656622471 0.26671571598967303
chr16 90354753 7561576 0.08368763954232712 0.4476109854726861
chr17 81195210 8877219 0.10933180664228838 0.5122370231995385
chr18 78077248 6307541 0.08078590321216239 1.3753625096733664
chr19 59128983 7701900 0.13025591865836758 0.867318175732522
chr20 63025520 7516375 0.11925923022927855 0.5021068007197271
chr21 48129895 3700320 0.07688194624151995 0.4040065203957794
chr22 51304566 3617719 0.07051456199824398 0.35237596563526485
chrMT 16571 384663 23.213022750588376 16.33078652217917
chrX 155270560 21949169 0.14136078983678554 0.5806437154285927
chrY 59373566 755970 0.012732433824170171 0.1801436478987663