BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238539.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 = 1,808,739
number of mapped reads = 1,575,280 (87.09%)
number of supplementary alignments = 15,564 (0.86%)
number of secondary alignments = 0
number of mapped bases = 94,671,070 bp
number of sequenced bases = 94,604,931 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 400,870
duplication rate = 19.14%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.0612
>>>>>>> ACTG content
number of A's = 23,115,924 bp (24.43%)
number of C's = 16,602,445 bp (17.55%)
number of T's = 31,966,697 bp (33.79%)
number of G's = 22,913,895 bp (24.22%)
number of N's = 5,970 bp (0.01%)
GC percentage = 41.77%
>>>>>>> Mismatches and indels
general error rate = 0.007
number of mismatches = 647,335
number of insertions = 6,175
mapped reads with insertion percentage = 0.39%
number of deletions = 38,938
mapped reads with deletion percentage = 2.44%
homopolymer indels = 40.33%
>>>>>>> Coverage
mean coverageData = 0.0306X
std coverageData = 0.5232X
There is a 1.63% of reference with a coverageData >= 1X
There is a 0.68% of reference with a coverageData >= 2X
There is a 0.34% of reference with a coverageData >= 3X
There is a 0.17% of reference with a coverageData >= 4X
There is a 0.09% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% 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 9297435 0.03730155199894166 0.41166908176450184
chr2 243199373 7362603 0.030273939069736005 1.3196331723458476
chr3 198022430 5169450 0.026105376042501852 0.2800749254749446
chr4 191154276 4862418 0.025437139580387937 0.2708619078046151
chr5 180915260 4964115 0.02743889597815021 0.28436410573151893
chr6 171115067 5565543 0.03252514870592898 0.5026010139168885
chr7 159138663 8714459 0.05476016221149225 0.5243112347140697
chr8 146364022 5783356 0.03951350831285574 0.4341665963214009
chr9 141213431 3471027 0.024580006132702774 0.2970126795139746
chr10 135534747 5972058 0.04406292948626672 0.39962203188200357
chr11 135006516 3149548 0.023328859178915484 0.2651311834362854
chr12 133851895 4214415 0.03148565808500507 0.30791637923860643
chr13 115169878 1846731 0.016034843763575054 0.35312750529922093
chr14 107349540 2984861 0.027805065582954525 0.293168718043906
chr15 102531392 2665288 0.025994848485037636 0.35278207594308575
chr16 90354753 1961071 0.021704126621872342 0.2709911745144313
chr17 81195210 1650788 0.020331100812474037 0.24262567144016817
chr18 78077248 4181529 0.053556306185381944 1.0280821583371114
chr19 59128983 1281257 0.021668848929804863 0.30793185228872044
chr20 63025520 1884749 0.029904537082756318 0.2992778910702922
chr21 48129895 1410595 0.029308083884246994 0.3033270583605872
chr22 51304566 654193 0.012751165266654823 0.18796172938771286
chrMT 16571 15740 0.9498521513487418 1.7551053814033672
chrX 155270560 5342535 0.03440790707523693 0.32372790665660495
chrY 59373566 265306 0.0044684194983336525 0.19854710003040354