BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524707.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 = 1,271,233
number of mapped reads = 1,163,815 (91.55%)
number of supplementary alignments = 4,048 (0.32%)
number of secondary alignments = 0
number of mapped bases = 68,429,590 bp
number of sequenced bases = 68,407,943 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 37,909
duplication rate = 2.34%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6888
>>>>>>> ACTG content
number of A's = 17,382,013 bp (25.41%)
number of C's = 13,202,986 bp (19.3%)
number of T's = 22,636,877 bp (33.09%)
number of G's = 15,176,773 bp (22.19%)
number of N's = 9,294 bp (0.01%)
GC percentage = 41.49%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 351,716
number of insertions = 4,975
mapped reads with insertion percentage = 0.42%
number of deletions = 13,410
mapped reads with deletion percentage = 1.14%
homopolymer indels = 43.21%
>>>>>>> Coverage
mean coverageData = 0.0221X
std coverageData = 0.2313X
There is a 2.03% of reference with a coverageData >= 1X
There is a 0.12% of reference with a coverageData >= 2X
There is a 0.01% 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 5496649 0.022052699319052047 0.39502636247629574
chr2 243199373 5801501 0.023854917586485717 0.33007465505343575
chr3 198022430 4562171 0.023038657792453107 0.16289344188809474
chr4 191154276 4467495 0.023371148652724882 0.18029672497550298
chr5 180915260 4178647 0.02309726111550789 0.16243900967863306
chr6 171115067 3991980 0.023329213902595732 0.1820679076245553
chr7 159138663 3824682 0.02403364416854501 0.25948671072683016
chr8 146364022 3457257 0.02362094832294237 0.2606105543707395
chr9 141213431 2861339 0.02026251313162981 0.1942074194393793
chr10 135534747 3290486 0.024277803831367316 0.23690761111669245
chr11 135006516 3127280 0.02316391899188036 0.19710840597618526
chr12 133851895 3086249 0.023057193176084657 0.1636113553420661
chr13 115169878 2156602 0.018725399709114913 0.14757537093972226
chr14 107349540 2036617 0.018971827918405612 0.14967028598211735
chr15 102531392 1912548 0.018653292057129196 0.1460115036545805
chr16 90354753 1979368 0.021906628420532565 0.16910856103152572
chr17 81195210 1825954 0.022488444823284527 0.16699859833442574
chr18 78077248 1824663 0.023369970724377992 0.3268879081360894
chr19 59128983 1380727 0.023351103468158753 0.30115166767665497
chr20 63025520 1441905 0.02287811350068988 0.1641029431208304
chr21 48129895 895020 0.018595926710415638 0.15607609130103756
chr22 51304566 770238 0.015013049715691971 0.1304784307346532
chrMT 16571 3984 0.24042001086234988 0.5720211320668249
chrX 155270560 3824221 0.024629401735911816 0.18219590277852415
chrY 59373566 232007 0.003907580690033002 0.1478823928909913