BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1708554.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,850,180
number of mapped reads = 3,168,086 (82.28%)
number of supplementary alignments = 93 (0%)
number of secondary alignments = 0
number of mapped bases = 157,980,729 bp
number of sequenced bases = 157,966,018 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 15,086
duplication rate = 0.47%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.3473
>>>>>>> ACTG content
number of A's = 49,068,057 bp (31.06%)
number of C's = 29,889,679 bp (18.92%)
number of T's = 48,832,236 bp (30.91%)
number of G's = 30,169,447 bp (19.1%)
number of N's = 6,599 bp (0%)
GC percentage = 38.02%
>>>>>>> Mismatches and indels
general error rate = 0.0017
number of mismatches = 250,024
number of insertions = 10,524
mapped reads with insertion percentage = 0.33%
number of deletions = 8,620
mapped reads with deletion percentage = 0.27%
homopolymer indels = 47.16%
>>>>>>> Coverage
mean coverageData = 0.051X
std coverageData = 0.2329X
There is a 4.83% of reference with a coverageData >= 1X
There is a 0.26% 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 11551605 0.04634534090087583 0.22277348083383458
chr2 243199373 14280009 0.05871729365025954 0.2492625809010046
chr3 198022430 11714868 0.059159298267373046 0.2496994258289581
chr4 191154276 12180571 0.06372115369263306 0.2590194970634441
chr5 180915260 10461466 0.05782522712567199 0.24711240016056032
chr6 171115067 10675712 0.06238908231266391 0.2565966575251822
chr7 159138663 8929745 0.056112982424641834 0.2440184287580289
chr8 146364022 8769658 0.05991676014478476 0.2519224461888535
chr9 141213431 6638861 0.04701295728732772 0.22415623337285362
chr10 135534747 6622997 0.04886567575176866 0.2266920088688048
chr11 135006516 7022485 0.05201589677345648 0.23496241397382397
chr12 133851895 7265339 0.05427894016741414 0.2398012842131594
chr13 115169878 6248454 0.05425423824795577 0.24050537090098587
chr14 107349540 4978993 0.04638113027778228 0.22284658288431272
chr15 102531392 4253300 0.04148290505994496 0.21035174514557026
chr16 90354753 2705270 0.029940538933242396 0.1780824850890281
chr17 81195210 2677103 0.03297119374406446 0.1868265599362588
chr18 78077248 4458054 0.05709799095377952 0.24530510373739475
chr19 59128983 1257599 0.021268740576850444 0.1491957274702686
chr20 63025520 2362944 0.03749186044002493 0.1992821957623896
chr21 48129895 1932374 0.04014914223270173 0.20758925531940806
chr22 51304566 866939 0.016897891700321566 0.13303796129758866
chrMT 16571 248 0.014965904290628206 0.12141633333037184
chrX 155270560 9897737 0.06374509758965254 0.2599921472974032
chrY 59373566 228398 0.0038467960640935733 0.06488957959788924