BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472513.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,363,566
number of mapped reads = 13,244,904 (99.11%)
number of supplementary alignments = 55,184 (0.41%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,640,749
number of mapped paired reads (second in pair) = 6,604,155
number of mapped paired reads (both in pair) = 13,178,256
number of mapped paired reads (singletons) = 66,648
number of mapped bases = 1,303,123,146 bp
number of sequenced bases = 1,302,943,426 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,909,134
duplication rate = 45.69%
>>>>>>> Insert size
mean insert size = 32,199.3083
std insert size = 1,788,827.1429
median insert size = 229
>>>>>>> Mapping quality
mean mapping quality = 55.1783
>>>>>>> ACTG content
number of A's = 359,226,775 bp (27.57%)
number of C's = 294,361,697 bp (22.59%)
number of T's = 357,004,258 bp (27.4%)
number of G's = 292,146,836 bp (22.42%)
number of N's = 203,860 bp (0.02%)
GC percentage = 45.01%
>>>>>>> Mismatches and indels
general error rate = 0.006
number of mismatches = 7,728,255
number of insertions = 69,142
mapped reads with insertion percentage = 0.52%
number of deletions = 67,358
mapped reads with deletion percentage = 0.5%
homopolymer indels = 44.56%
>>>>>>> Coverage
mean coverageData = 0.4209X
std coverageData = 14.4735X
There is a 4.2% of reference with a coverageData >= 1X
There is a 1.86% of reference with a coverageData >= 2X
There is a 0.8% of reference with a coverageData >= 3X
There is a 0.59% of reference with a coverageData >= 4X
There is a 0.44% of reference with a coverageData >= 5X
There is a 0.4% of reference with a coverageData >= 6X
There is a 0.36% of reference with a coverageData >= 7X
There is a 0.34% of reference with a coverageData >= 8X
There is a 0.32% of reference with a coverageData >= 9X
There is a 0.31% of reference with a coverageData >= 10X
There is a 0.3% of reference with a coverageData >= 11X
There is a 0.29% of reference with a coverageData >= 12X
There is a 0.28% of reference with a coverageData >= 13X
There is a 0.27% of reference with a coverageData >= 14X
There is a 0.26% of reference with a coverageData >= 15X
There is a 0.26% of reference with a coverageData >= 16X
There is a 0.25% of reference with a coverageData >= 17X
There is a 0.24% of reference with a coverageData >= 18X
There is a 0.24% of reference with a coverageData >= 19X
There is a 0.23% of reference with a coverageData >= 20X
There is a 0.23% of reference with a coverageData >= 21X
There is a 0.22% of reference with a coverageData >= 22X
There is a 0.22% of reference with a coverageData >= 23X
There is a 0.21% of reference with a coverageData >= 24X
There is a 0.21% of reference with a coverageData >= 25X
There is a 0.2% of reference with a coverageData >= 26X
There is a 0.2% of reference with a coverageData >= 27X
There is a 0.2% of reference with a coverageData >= 28X
There is a 0.19% of reference with a coverageData >= 29X
There is a 0.19% of reference with a coverageData >= 30X
There is a 0.19% of reference with a coverageData >= 31X
There is a 0.18% of reference with a coverageData >= 32X
There is a 0.18% of reference with a coverageData >= 33X
There is a 0.18% of reference with a coverageData >= 34X
There is a 0.17% of reference with a coverageData >= 35X
There is a 0.17% of reference with a coverageData >= 36X
There is a 0.17% of reference with a coverageData >= 37X
There is a 0.17% of reference with a coverageData >= 38X
There is a 0.16% of reference with a coverageData >= 39X
There is a 0.16% of reference with a coverageData >= 40X
There is a 0.16% of reference with a coverageData >= 41X
There is a 0.16% of reference with a coverageData >= 42X
There is a 0.16% of reference with a coverageData >= 43X
There is a 0.15% of reference with a coverageData >= 44X
There is a 0.15% of reference with a coverageData >= 45X
There is a 0.15% of reference with a coverageData >= 46X
There is a 0.15% of reference with a coverageData >= 47X
There is a 0.15% of reference with a coverageData >= 48X
There is a 0.14% of reference with a coverageData >= 49X
There is a 0.14% of reference with a coverageData >= 50X
There is a 0.14% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 141449152 0.5674976914099644 23.236580526049618
chr2 243199373 94242264 0.3875103082605398 13.021689366185214
chr3 198022430 154294149 0.7791751116275061 17.65655386520079
chr4 191154276 56057708 0.29325897998745265 11.879270659942314
chr5 180915260 69019784 0.38150338451272714 14.157493201103083
chr6 171115067 89909246 0.5254314980924503 13.095470604419027
chr7 159138663 51418721 0.32310640312467626 10.66163173549028
chr8 146364022 68291383 0.4665858594675678 15.319245007011745
chr9 141213431 74172249 0.5252492519638589 13.647287816332398
chr10 135534747 30919128 0.2281269466640905 7.459544120851585
chr11 135006516 53559188 0.3967155777873714 16.316618400992844
chr12 133851895 61849077 0.46207098524828505 13.267772029426304
chr13 115169878 37222468 0.3231962093421684 16.725147418524955
chr14 107349540 35032312 0.3263387248794918 10.412514639141966
chr15 102531392 36012823 0.3512370435778342 13.220487081020433
chr16 90354753 45318241 0.5015590159379884 15.451601735801246
chr17 81195210 45441110 0.5596525952700905 15.773607862969847
chr18 78077248 19821668 0.25387252378567443 10.833328592307712
chr19 59128983 29320443 0.49587260785459475 16.88227824792546
chr20 63025520 31522558 0.5001554608355473 18.86285171612025
chr21 48129895 5083619 0.105622898200796 4.078598124624634
chr22 51304566 14706609 0.2866530242162072 8.963660882718294
chrMT 16571 1764 0.10645102890591998 0.42889286643899965
chrX 155270560 54883855 0.3534723839470921 9.659889255259133
chrY 59373566 3573627 0.060188855761164825 4.304560231358695