BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008807.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 = 1,354,947
number of mapped reads = 860,484 (63.51%)
number of supplementary alignments = 9,137 (0.67%)
number of secondary alignments = 0
number of mapped bases = 57,811,800 bp
number of sequenced bases = 57,784,431 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 39,372
duplication rate = 3.74%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.4929
>>>>>>> ACTG content
number of A's = 15,780,246 bp (27.31%)
number of C's = 11,146,736 bp (19.29%)
number of T's = 17,825,435 bp (30.85%)
number of G's = 12,944,347 bp (22.4%)
number of N's = 87,667 bp (0.15%)
GC percentage = 41.69%
>>>>>>> Mismatches and indels
general error rate = 0.0086
number of mismatches = 488,328
number of insertions = 4,220
mapped reads with insertion percentage = 0.49%
number of deletions = 15,325
mapped reads with deletion percentage = 1.76%
homopolymer indels = 46.31%
>>>>>>> Coverage
mean coverageData = 0.0187X
std coverageData = 0.2118X
There is a 1.46% of reference with a coverageData >= 1X
There is a 0.28% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% 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 4157520 0.016680078803093534 0.285839145187411
chr2 243199373 4946203 0.02033805819063522 0.25875561009731485
chr3 198022430 4181057 0.0211140576347841 0.17990117539358924
chr4 191154276 4130376 0.021607552216095862 0.18485634496052403
chr5 180915260 2984933 0.016499067021764777 0.15848781165732953
chr6 171115067 3334420 0.019486419626624698 0.18957488075002188
chr7 159138663 3053150 0.019185469718317288 0.2537193993113542
chr8 146364022 2850633 0.019476323218283794 0.23737942075061882
chr9 141213431 2299932 0.016286921036569108 0.19782916813246382
chr10 135534747 3073396 0.02267607435014432 0.24741497600153667
chr11 135006516 2429419 0.01799482774594376 0.19778621780048705
chr12 133851895 2442077 0.01824462029469213 0.16818322038273537
chr13 115169878 2108283 0.018305854244284256 0.16594681121456195
chr14 107349540 1707452 0.015905536251017004 0.16660335856878694
chr15 102531392 1566144 0.015274775553617764 0.15195669045276372
chr16 90354753 1427746 0.01580155943760922 0.1668513691124406
chr17 81195210 1474906 0.018164938547483283 0.1746537462316163
chr18 78077248 1392806 0.01783882034366785 0.33011473853614864
chr19 59128983 1115908 0.018872436889367773 0.22221129677750265
chr20 63025520 1184416 0.018792641456984407 0.174197494618448
chr21 48129895 729275 0.015152225036019713 0.1604195982063321
chr22 51304566 709426 0.013827736112220499 0.14495239875424842
chrMT 16571 102583 6.190513547764167 4.254137455813645
chrX 155270560 4252604 0.02738834715351062 0.20867119961055308
chrY 59373566 157135 0.0026465481288423876 0.07642797415740965