BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524313.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 = 679,842
number of mapped reads = 621,244 (91.38%)
number of supplementary alignments = 2,737 (0.4%)
number of secondary alignments = 0
number of mapped bases = 36,168,466 bp
number of sequenced bases = 36,158,806 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,871
duplication rate = 1.18%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.6318
>>>>>>> ACTG content
number of A's = 8,555,644 bp (23.66%)
number of C's = 6,862,981 bp (18.98%)
number of T's = 11,534,820 bp (31.9%)
number of G's = 9,200,930 bp (25.45%)
number of N's = 4,431 bp (0.01%)
GC percentage = 44.43%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 184,171
number of insertions = 2,373
mapped reads with insertion percentage = 0.38%
number of deletions = 5,955
mapped reads with deletion percentage = 0.95%
homopolymer indels = 42.17%
>>>>>>> Coverage
mean coverageData = 0.0117X
std coverageData = 0.1397X
There is a 1.11% of reference with a coverageData >= 1X
There is a 0.04% 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 3055672 0.012259435855126717 0.23272312101533016
chr2 243199373 2342964 0.009633922863773172 0.15350686985529993
chr3 198022430 2554661 0.012900866836145783 0.11723728219458582
chr4 191154276 1892732 0.009901593830943127 0.107098939617522
chr5 180915260 2133307 0.011791747141728122 0.11230505982608036
chr6 171115067 2315731 0.013533179985839586 0.12529225686276868
chr7 159138663 1648459 0.010358632961494718 0.15604218310301765
chr8 146364022 3755543 0.02565892183531278 0.1878695484527911
chr9 141213431 1497510 0.010604586188405832 0.11897422558427165
chr10 135534747 1843957 0.013605049928635643 0.14210073215766167
chr11 135006516 1742716 0.012908384362722167 0.13137205486640877
chr12 133851895 1411770 0.01054725448601232 0.10676851614183108
chr13 115169878 910377 0.007904644997540069 0.09163681903324422
chr14 107349540 757856 0.007059704214848056 0.08868054933332259
chr15 102531392 1087369 0.01060523005481092 0.1073359404584957
chr16 90354753 1129560 0.012501389937948255 0.1196923532061572
chr17 81195210 1130192 0.01391944179958399 0.12767837782202254
chr18 78077248 849365 0.010878521230666327 0.1765287881546466
chr19 59128983 647615 0.010952581410033722 0.16231521797806178
chr20 63025520 814243 0.01291925873836503 0.11811727809429656
chr21 48129895 511451 0.010626472382705178 0.11128590166334208
chr22 51304566 263634 0.005138606961415481 0.07422633871606846
chrMT 16571 1634 0.09860599843099391 0.30493673098970836
chrX 155270560 1763143 0.011355294912313062 0.11464011794237156
chrY 59373566 107005 0.0018022330004568027 0.061528289003093095