BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524828.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,501,959
number of mapped reads = 1,364,042 (90.82%)
number of supplementary alignments = 4,641 (0.31%)
number of secondary alignments = 0
number of mapped bases = 78,490,303 bp
number of sequenced bases = 78,465,863 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 43,471
duplication rate = 2.44%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7838
>>>>>>> ACTG content
number of A's = 19,667,972 bp (25.07%)
number of C's = 14,017,349 bp (17.86%)
number of T's = 24,515,608 bp (31.24%)
number of G's = 20,254,492 bp (25.81%)
number of N's = 10,442 bp (0.01%)
GC percentage = 43.68%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 390,474
number of insertions = 5,666
mapped reads with insertion percentage = 0.41%
number of deletions = 15,205
mapped reads with deletion percentage = 1.11%
homopolymer indels = 41.63%
>>>>>>> Coverage
mean coverageData = 0.0254X
std coverageData = 0.22X
There is a 2.28% of reference with a coverageData >= 1X
There is a 0.19% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% 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 6298437 0.02526949371171276 0.2629046838000356
chr2 243199373 6609195 0.02717603634611344 0.33524439297420416
chr3 198022430 5112201 0.025816272429340453 0.17661740647663676
chr4 191154276 4989742 0.026103219370305897 0.20329509522739375
chr5 180915260 4641098 0.025653435757713308 0.174416474158527
chr6 171115067 4423886 0.02585328152312853 0.18904997477851088
chr7 159138663 4314830 0.027113649936847842 0.26667016529854176
chr8 146364022 3895385 0.02661436155396167 0.1994980974651508
chr9 141213431 3319341 0.023505844851259228 0.19968163441865336
chr10 135534747 3862230 0.028496234991311858 0.2724325014414
chr11 135006516 3582040 0.026532349001584486 0.20332073354247457
chr12 133851895 3594021 0.026850729307941437 0.18029017352886673
chr13 115169878 2440412 0.021189672528783957 0.15893078472509498
chr14 107349540 2345753 0.021851542167763364 0.16477924979753672
chr15 102531392 2277201 0.022209793074885787 0.16572846654727708
chr16 90354753 2410224 0.02667512134087733 0.19409739854285876
chr17 81195210 2225807 0.027413033355046437 0.18762105013628005
chr18 78077248 2067604 0.026481517381350326 0.2892817846960273
chr19 59128983 1757530 0.02972366360503782 0.24215133733622715
chr20 63025520 1712291 0.027168216938154577 0.1894464050114236
chr21 48129895 1015182 0.021092545495891898 0.17808427063045207
chr22 51304566 1014748 0.019778902330057718 0.15528967861775572
chrMT 16571 18831 1.1363828374871765 1.2187458492041152
chrX 155270560 4300348 0.02769583622291309 0.1934000578107652
chrY 59373566 261966 0.00441216550813202 0.1286646115916162