BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524538.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 = 935,654
number of mapped reads = 857,023 (91.6%)
number of supplementary alignments = 2,916 (0.31%)
number of secondary alignments = 0
number of mapped bases = 50,011,651 bp
number of sequenced bases = 49,995,945 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 25,201
duplication rate = 2.2%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9743
>>>>>>> ACTG content
number of A's = 12,330,533 bp (24.66%)
number of C's = 9,389,805 bp (18.78%)
number of T's = 16,045,728 bp (32.09%)
number of G's = 12,229,215 bp (24.46%)
number of N's = 664 bp (0%)
GC percentage = 43.24%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 254,978
number of insertions = 3,192
mapped reads with insertion percentage = 0.37%
number of deletions = 9,323
mapped reads with deletion percentage = 1.08%
homopolymer indels = 44.13%
>>>>>>> Coverage
mean coverageData = 0.0162X
std coverageData = 0.1766X
There is a 1.49% of reference with a coverageData >= 1X
There is a 0.08% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 4854572 0.01947666962883916 0.306178129292855
chr2 243199373 3878060 0.015946011505547756 0.1886831187364303
chr3 198022430 2730156 0.013787104824438323 0.12456107872125015
chr4 191154276 2761794 0.014447984412339278 0.14005918545650178
chr5 180915260 2731442 0.015097908269319017 0.13058472067106672
chr6 171115067 2144189 0.01253068498053418 0.14039278367348645
chr7 159138663 2472976 0.015539756042816572 0.204984567535962
chr8 146364022 5042191 0.03444966140654429 0.2193867236679803
chr9 141213431 2087161 0.014780187587114146 0.15130649583028838
chr10 135534747 2593153 0.019132754200662655 0.18249801875025018
chr11 135006516 1714075 0.012696239046713863 0.15807719032497947
chr12 133851895 2278423 0.017021970439790934 0.1391498008324324
chr13 115169878 1098538 0.009538414202366351 0.10283900691236944
chr14 107349540 1198377 0.011163317513982826 0.11371377616734746
chr15 102531392 1327675 0.012948961036245368 0.12035476913011349
chr16 90354753 1543841 0.017086439271213547 0.1438112522379019
chr17 81195210 1734796 0.021365743126965247 0.1602717802488239
chr18 78077248 1165250 0.014924322127747126 0.2594394478236993
chr19 59128983 1020513 0.017259099484257998 0.22767619281081355
chr20 63025520 1423624 0.022588056393664027 0.15990300537041394
chr21 48129895 674429 0.014012683800785354 0.13537418116350206
chr22 51304566 415238 0.008093587615574022 0.09497052686583567
chrMT 16571 2632 0.1588316939231187 0.42788809905036435
chrX 155270560 2943418 0.018956703704810493 0.15567467907721286
chrY 59373566 175128 0.002949595447913639 0.09924712549064689