BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR618619.sorted.bam
outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 38,074,480
number of mapped reads = 34,772,636 (91.33%)
number of supplementary alignments = 186,782 (0.49%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 17,656,723
number of mapped paired reads (second in pair) = 17,115,913
number of mapped paired reads (both in pair) = 33,655,580
number of mapped paired reads (singletons) = 1,117,056
number of mapped bases = 3,260,290,758 bp
number of sequenced bases = 3,257,983,348 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,046,446
duplication rate = 30.01%
>>>>>>> Insert size
mean insert size = 122,494.1486
std insert size = 3,518,218.9924
median insert size = 213
>>>>>>> Mapping quality
mean mapping quality = 52.074
>>>>>>> ACTG content
number of A's = 895,318,695 bp (27.48%)
number of C's = 705,174,194 bp (21.64%)
number of T's = 910,682,558 bp (27.95%)
number of G's = 744,485,558 bp (22.85%)
number of N's = 2,322,343 bp (0.07%)
GC percentage = 44.5%
>>>>>>> Mismatches and indels
general error rate = 0.014
number of mismatches = 44,709,591
number of insertions = 628,266
mapped reads with insertion percentage = 1.78%
number of deletions = 1,701,198
mapped reads with deletion percentage = 4.77%
homopolymer indels = 52.6%
>>>>>>> Coverage
mean coverageData = 1.0532X
std coverageData = 4.5869X
There is a 21.78% of reference with a coverageData >= 1X
There is a 14.87% of reference with a coverageData >= 2X
There is a 11.01% of reference with a coverageData >= 3X
There is a 8.57% of reference with a coverageData >= 4X
There is a 6.83% of reference with a coverageData >= 5X
There is a 5.56% of reference with a coverageData >= 6X
There is a 4.58% of reference with a coverageData >= 7X
There is a 3.83% of reference with a coverageData >= 8X
There is a 3.23% of reference with a coverageData >= 9X
There is a 2.75% of reference with a coverageData >= 10X
There is a 2.35% of reference with a coverageData >= 11X
There is a 2.03% of reference with a coverageData >= 12X
There is a 1.75% of reference with a coverageData >= 13X
There is a 1.53% of reference with a coverageData >= 14X
There is a 1.34% of reference with a coverageData >= 15X
There is a 1.18% of reference with a coverageData >= 16X
There is a 1.04% of reference with a coverageData >= 17X
There is a 0.92% of reference with a coverageData >= 18X
There is a 0.82% of reference with a coverageData >= 19X
There is a 0.73% of reference with a coverageData >= 20X
There is a 0.65% of reference with a coverageData >= 21X
There is a 0.59% of reference with a coverageData >= 22X
There is a 0.53% of reference with a coverageData >= 23X
There is a 0.48% of reference with a coverageData >= 24X
There is a 0.43% of reference with a coverageData >= 25X
There is a 0.39% of reference with a coverageData >= 26X
There is a 0.35% of reference with a coverageData >= 27X
There is a 0.32% of reference with a coverageData >= 28X
There is a 0.29% of reference with a coverageData >= 29X
There is a 0.27% of reference with a coverageData >= 30X
There is a 0.24% of reference with a coverageData >= 31X
There is a 0.22% of reference with a coverageData >= 32X
There is a 0.21% of reference with a coverageData >= 33X
There is a 0.19% of reference with a coverageData >= 34X
There is a 0.17% of reference with a coverageData >= 35X
There is a 0.16% of reference with a coverageData >= 36X
There is a 0.15% of reference with a coverageData >= 37X
There is a 0.14% of reference with a coverageData >= 38X
There is a 0.13% of reference with a coverageData >= 39X
There is a 0.12% of reference with a coverageData >= 40X
There is a 0.11% of reference with a coverageData >= 41X
There is a 0.1% of reference with a coverageData >= 42X
There is a 0.09% of reference with a coverageData >= 43X
There is a 0.09% of reference with a coverageData >= 44X
There is a 0.08% of reference with a coverageData >= 45X
There is a 0.08% of reference with a coverageData >= 46X
There is a 0.07% of reference with a coverageData >= 47X
There is a 0.07% of reference with a coverageData >= 48X
There is a 0.06% of reference with a coverageData >= 49X
There is a 0.06% of reference with a coverageData >= 50X
There is a 0.06% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 302275036 1.212735337578156 8.238624661597505
chr2 243199373 291134590 1.1971025517405425 4.7108810784873105
chr3 198022430 222590067 1.12406492032241 3.7290598065597083
chr4 191154276 179044099 0.9366471038293698 3.4346952837017466
chr5 180915260 194581626 1.075540150676068 3.6291058780415457
chr6 171115067 184842149 1.0802213518696164 4.060293015168729
chr7 159138663 172965866 1.0868877665511114 4.029342721384208
chr8 146364022 167044057 1.141291792323116 3.9625486273592756
chr9 141213431 145122850 1.0276844700416634 5.342330839667897
chr10 135534747 173493429 1.2800660556809096 4.323578685072117
chr11 135006516 167997362 1.2443648423606457 4.617409987372665
chr12 133851895 151679398 1.133188274996032 4.178890070000662
chr13 115169878 94007083 0.816247135383785 3.158260566569485
chr14 107349540 102795726 0.9575795667126287 3.62767800251361
chr15 102531392 107371865 1.047209668235071 3.7829314594879944
chr16 90354753 116480333 1.2891445013412852 5.03543480547251
chr17 81195210 103643910 1.2764781321459726 4.557662378988398
chr18 78077248 88542349 1.1340352185568836 5.336353285989698
chr19 59128983 64549606 1.091674551547758 4.537326237418829
chr20 63025520 93466288 1.4829911439048817 4.826441646180815
chr21 48129895 44412670 0.922766816757028 4.901752963578041
chr22 51304566 54080199 1.0541010911192583 4.224235727736872
chrMT 16571 4212 0.25417898738760486 1.8269764929342467
chrX 155270560 5766804 0.03714035680685379 1.0294801600255044
chrY 59373566 32399184 0.5456836464900895 3.0624198255759136