BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3084347.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,974,509
number of mapped reads = 1,801,027 (91.21%)
number of supplementary alignments = 10,644 (0.54%)
number of secondary alignments = 0
number of mapped bases = 121,685,643 bp
number of sequenced bases = 121,642,043 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 58,371
duplication rate = 2.78%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6711
>>>>>>> ACTG content
number of A's = 34,446,401 bp (28.32%)
number of C's = 22,984,706 bp (18.9%)
number of T's = 37,778,426 bp (31.06%)
number of G's = 26,282,756 bp (21.61%)
number of N's = 149,754 bp (0.12%)
GC percentage = 40.5%
>>>>>>> Mismatches and indels
general error rate = 0.0097
number of mismatches = 1,160,404
number of insertions = 8,360
mapped reads with insertion percentage = 0.46%
number of deletions = 24,805
mapped reads with deletion percentage = 1.36%
homopolymer indels = 48.09%
>>>>>>> Coverage
mean coverageData = 0.0393X
std coverageData = 0.2802X
There is a 3.38% of reference with a coverageData >= 1X
There is a 0.42% 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 11998658 0.048138929210531436 0.44767717628502346
chr2 243199373 11775754 0.0484201659516614 0.30849776749706886
chr3 198022430 8200396 0.041411450207938565 0.2311394370095078
chr4 191154276 5978464 0.031275596471616464 0.2052845237350289
chr5 180915260 6246461 0.0345269989938936 0.20941652994271975
chr6 171115067 5765413 0.03369319313067855 0.22008117750098927
chr7 159138663 6767205 0.04252395283728128 0.36334324700873993
chr8 146364022 5954864 0.04068529901426185 0.27777024033258146
chr9 141213431 4371891 0.03095945597412756 0.23972311137818808
chr10 135534747 8712739 0.06428417208761972 0.3891988563084629
chr11 135006516 6766477 0.05011963274424473 0.28862038261827916
chr12 133851895 6366213 0.04756162025199569 0.24682695795448875
chr13 115169878 2944224 0.02556418441287226 0.17889299872304035
chr14 107349540 3262166 0.03038826249278758 0.1999694648007585
chr15 102531392 2654269 0.025887378959996953 0.18371132895225198
chr16 90354753 2633791 0.029149446072859055 0.20183890824550355
chr17 81195210 3136801 0.038632833143728555 0.23082427325577146
chr18 78077248 3257701 0.04172407562315721 0.3487411770504244
chr19 59128983 2342510 0.03961695062470464 0.3363639520324222
chr20 63025520 2347596 0.03724834003749592 0.21932022888251232
chr21 48129895 1215963 0.025264193906926247 0.18362289568259896
chr22 51304566 966365 0.018835847865860515 0.1532768177323656
chrMT 16571 117005 7.060829159374811 4.768938632583335
chrX 155270560 7654034 0.049294818026031466 0.26815556060824
chrY 59373566 248683 0.0041884464207522926 0.09166491403779647