BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8438285.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 811,866,872
number of mapped reads = 808,949,403 (99.64%)
number of supplementary alignments = 23,291,031 (2.87%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 404,695,150
number of mapped paired reads (second in pair) = 404,254,253
number of mapped paired reads (both in pair) = 807,370,426
number of mapped paired reads (singletons) = 1,578,977
number of mapped bases = 93,547,877,887 bp
number of sequenced bases = 93,525,337,873 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 318,931,480
duplication rate = 37.81%
>>>>>>> Insert size
mean insert size = 295,266.0907
std insert size = 5,360,344.5922
median insert size = 146
>>>>>>> Mapping quality
mean mapping quality = 53.0547
>>>>>>> ACTG content
number of A's = 28,732,085,707 bp (30.72%)
number of C's = 18,165,577,597 bp (19.42%)
number of T's = 27,965,181,534 bp (29.9%)
number of G's = 18,662,260,163 bp (19.95%)
number of N's = 232,872 bp (0%)
GC percentage = 39.38%
>>>>>>> Mismatches and indels
general error rate = 0.0031
number of mismatches = 265,807,274
number of insertions = 13,300,163
mapped reads with insertion percentage = 1.63%
number of deletions = 9,468,400
mapped reads with deletion percentage = 1.16%
homopolymer indels = 47.76%
>>>>>>> Coverage
mean coverageData = 30.2187X
std coverageData = 389.0596X
There is a 86.86% of reference with a coverageData >= 1X
There is a 84.62% of reference with a coverageData >= 2X
There is a 81.62% of reference with a coverageData >= 3X
There is a 79.12% of reference with a coverageData >= 4X
There is a 76.5% of reference with a coverageData >= 5X
There is a 74.04% of reference with a coverageData >= 6X
There is a 71.6% of reference with a coverageData >= 7X
There is a 69.26% of reference with a coverageData >= 8X
There is a 66.98% of reference with a coverageData >= 9X
There is a 64.77% of reference with a coverageData >= 10X
There is a 62.63% of reference with a coverageData >= 11X
There is a 60.55% of reference with a coverageData >= 12X
There is a 58.55% of reference with a coverageData >= 13X
There is a 56.61% of reference with a coverageData >= 14X
There is a 54.74% of reference with a coverageData >= 15X
There is a 52.94% of reference with a coverageData >= 16X
There is a 51.19% of reference with a coverageData >= 17X
There is a 49.51% of reference with a coverageData >= 18X
There is a 47.89% of reference with a coverageData >= 19X
There is a 46.33% of reference with a coverageData >= 20X
There is a 44.82% of reference with a coverageData >= 21X
There is a 43.37% of reference with a coverageData >= 22X
There is a 41.98% of reference with a coverageData >= 23X
There is a 40.63% of reference with a coverageData >= 24X
There is a 39.33% of reference with a coverageData >= 25X
There is a 38.08% of reference with a coverageData >= 26X
There is a 36.88% of reference with a coverageData >= 27X
There is a 35.72% of reference with a coverageData >= 28X
There is a 34.6% of reference with a coverageData >= 29X
There is a 33.53% of reference with a coverageData >= 30X
There is a 32.49% of reference with a coverageData >= 31X
There is a 31.5% of reference with a coverageData >= 32X
There is a 30.53% of reference with a coverageData >= 33X
There is a 29.61% of reference with a coverageData >= 34X
There is a 28.72% of reference with a coverageData >= 35X
There is a 27.86% of reference with a coverageData >= 36X
There is a 27.03% of reference with a coverageData >= 37X
There is a 26.23% of reference with a coverageData >= 38X
There is a 25.46% of reference with a coverageData >= 39X
There is a 24.71% of reference with a coverageData >= 40X
There is a 24% of reference with a coverageData >= 41X
There is a 23.3% of reference with a coverageData >= 42X
There is a 22.64% of reference with a coverageData >= 43X
There is a 21.99% of reference with a coverageData >= 44X
There is a 21.37% of reference with a coverageData >= 45X
There is a 20.77% of reference with a coverageData >= 46X
There is a 20.19% of reference with a coverageData >= 47X
There is a 19.63% of reference with a coverageData >= 48X
There is a 19.08% of reference with a coverageData >= 49X
There is a 18.56% of reference with a coverageData >= 50X
There is a 18.05% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 7249253048 29.084192524439086 43.03510751437369
chr2 243199373 8532497871 35.08437446094896 1380.9135297377754
chr3 198022430 7131811037 36.015167761551055 42.4675356003486
chr4 191154276 6798281526 35.564370665712964 39.7145696102404
chr5 180915260 6328993427 34.983192832931834 42.49239764791639
chr6 171115067 5997096695 35.047157448735945 42.66617896866042
chr7 159138663 4824542372 30.3165948553935 40.43635007075707
chr8 146364022 5001467225 34.171425167586605 41.04825639327484
chr9 141213431 3946811420 27.949263692913178 40.093028415811276
chr10 135534747 3713240401 27.39696264751946 36.23033639690068
chr11 135006516 4314739741 31.959492540345238 41.019807291911796
chr12 133851895 4315287240 32.239268932277724 42.25745573150935
chr13 115169878 3234022211 28.08045182612766 37.27943006128368
chr14 107349540 3005538642 27.997685337077364 41.0571593227795
chr15 102531392 2425174999 23.652999844184308 37.669910266783496
chr16 90354753 1656825198 18.33689034598988 28.66525377319641
chr17 81195210 1468931168 18.091352531756492 29.38562856545292
chr18 78077248 2383313886 30.525075448355967 36.89619499851619
chr19 59128983 700956221 11.854697737655998 20.13983240692697
chr20 63025520 1387427929 22.01374822452873 33.78705631680175
chr21 48129895 962057608 19.98877429506131 32.39914213441003
chr22 51304566 456296770 8.893882271609119 22.032507524776925
chrMT 16571 152723 9.216281455554885 6.268133843755029
chrX 155270560 7644368195 49.23256665655099 59.876153373079134
chrY 59373566 68790334 1.1586020283841465 7.288296091753808