BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5365336.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 144,680,966
number of mapped reads = 142,032,397 (98.17%)
number of supplementary alignments = 1,201,693 (0.83%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 71,286,512
number of mapped paired reads (second in pair) = 70,745,885
number of mapped paired reads (both in pair) = 141,255,144
number of mapped paired reads (singletons) = 777,253
number of mapped bases = 18,710,091,707 bp
number of sequenced bases = 18,703,268,585 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 67,045,914
duplication rate = 30.45%
>>>>>>> Insert size
mean insert size = 81,853.4701
std insert size = 2,828,064.9044
median insert size = 206
>>>>>>> Mapping quality
mean mapping quality = 54.2338
>>>>>>> ACTG content
number of A's = 5,545,374,676 bp (29.65%)
number of C's = 3,756,584,941 bp (20.09%)
number of T's = 5,455,273,271 bp (29.17%)
number of G's = 3,945,366,076 bp (21.09%)
number of N's = 669,621 bp (0%)
GC percentage = 41.18%
>>>>>>> Mismatches and indels
general error rate = 0.0078
number of mismatches = 135,635,727
number of insertions = 5,458,247
mapped reads with insertion percentage = 3.73%
number of deletions = 2,893,726
mapped reads with deletion percentage = 1.97%
homopolymer indels = 50%
>>>>>>> Coverage
mean coverageData = 6.0439X
std coverageData = 62.584X
There is a 69.76% of reference with a coverageData >= 1X
There is a 64.08% of reference with a coverageData >= 2X
There is a 56.81% of reference with a coverageData >= 3X
There is a 51.23% of reference with a coverageData >= 4X
There is a 45.06% of reference with a coverageData >= 5X
There is a 40.03% of reference with a coverageData >= 6X
There is a 34.9% of reference with a coverageData >= 7X
There is a 30.68% of reference with a coverageData >= 8X
There is a 26.58% of reference with a coverageData >= 9X
There is a 23.17% of reference with a coverageData >= 10X
There is a 19.96% of reference with a coverageData >= 11X
There is a 17.29% of reference with a coverageData >= 12X
There is a 14.84% of reference with a coverageData >= 13X
There is a 12.79% of reference with a coverageData >= 14X
There is a 10.94% of reference with a coverageData >= 15X
There is a 9.39% of reference with a coverageData >= 16X
There is a 8% of reference with a coverageData >= 17X
There is a 6.85% of reference with a coverageData >= 18X
There is a 5.83% of reference with a coverageData >= 19X
There is a 4.98% of reference with a coverageData >= 20X
There is a 4.23% of reference with a coverageData >= 21X
There is a 3.61% of reference with a coverageData >= 22X
There is a 3.07% of reference with a coverageData >= 23X
There is a 2.62% of reference with a coverageData >= 24X
There is a 2.22% of reference with a coverageData >= 25X
There is a 1.9% of reference with a coverageData >= 26X
There is a 1.62% of reference with a coverageData >= 27X
There is a 1.38% of reference with a coverageData >= 28X
There is a 1.18% of reference with a coverageData >= 29X
There is a 1.02% of reference with a coverageData >= 30X
There is a 0.87% of reference with a coverageData >= 31X
There is a 0.75% of reference with a coverageData >= 32X
There is a 0.65% of reference with a coverageData >= 33X
There is a 0.56% of reference with a coverageData >= 34X
There is a 0.49% of reference with a coverageData >= 35X
There is a 0.42% of reference with a coverageData >= 36X
There is a 0.37% of reference with a coverageData >= 37X
There is a 0.33% of reference with a coverageData >= 38X
There is a 0.29% of reference with a coverageData >= 39X
There is a 0.25% of reference with a coverageData >= 40X
There is a 0.23% of reference with a coverageData >= 41X
There is a 0.2% of reference with a coverageData >= 42X
There is a 0.18% of reference with a coverageData >= 43X
There is a 0.16% of reference with a coverageData >= 44X
There is a 0.15% of reference with a coverageData >= 45X
There is a 0.13% of reference with a coverageData >= 46X
There is a 0.12% of reference with a coverageData >= 47X
There is a 0.11% of reference with a coverageData >= 48X
There is a 0.1% of reference with a coverageData >= 49X
There is a 0.1% of reference with a coverageData >= 50X
There is a 0.09% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1596122767 6.403686219903139 164.51492660210815
chr2 243199373 1635938706 6.7267389953344985 38.05055027188731
chr3 198022430 1257154406 6.348545495578455 8.935546366703772
chr4 191154276 1222435099 6.395018330638861 28.79949175521167
chr5 180915260 1123281968 6.208884579443437 8.179246179958131
chr6 171115067 1112912679 6.503884774798937 25.67637431400524
chr7 159138663 1013663903 6.369689702621167 45.584102952309244
chr8 146364022 939204924 6.416911145008027 20.54671256134967
chr9 141213431 810858518 5.74207787643089 63.046096580253646
chr10 135534747 992374088 7.321916408638738 130.36061424735055
chr11 135006516 883011220 6.540508163324502 39.974770609769514
chr12 133851895 896541327 6.698009968405752 33.61111083753117
chr13 115169878 581645858 5.050329722499142 6.573683660219889
chr14 107349540 574470005 5.35139698782128 7.41479368496883
chr15 102531392 546358663 5.328696434746541 17.570156799084344
chr16 90354753 551711294 6.106057243053943 19.858871614595344
chr17 81195210 569297354 7.011464764978131 31.029116054253922
chr18 78077248 511794377 6.554974593879129 63.4293597417939
chr19 59128983 378853826 6.407244075210968 82.93948003528551
chr20 63025520 399100376 6.332361494201079 12.30086820104994
chr21 48129895 248521886 5.1635659292421066 20.647833384721142
chr22 51304566 240321643 4.684215494581905 18.265687333889133
chrMT 16571 6631942 400.2137469072476 89.41314015113619
chrX 155270560 473857870 3.0518204481261613 13.028508903839278
chrY 59373566 144027008 2.4257766158091294 49.763822240722