BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524939.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 = 985,230
number of mapped reads = 905,134 (91.87%)
number of supplementary alignments = 3,965 (0.4%)
number of secondary alignments = 0
number of mapped bases = 52,751,910 bp
number of sequenced bases = 52,734,817 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 34,559
duplication rate = 2.99%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8554
>>>>>>> ACTG content
number of A's = 13,849,749 bp (26.26%)
number of C's = 9,448,770 bp (17.92%)
number of T's = 16,517,999 bp (31.32%)
number of G's = 12,917,892 bp (24.5%)
number of N's = 407 bp (0%)
GC percentage = 42.41%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 268,929
number of insertions = 3,699
mapped reads with insertion percentage = 0.41%
number of deletions = 10,086
mapped reads with deletion percentage = 1.11%
homopolymer indels = 41.94%
>>>>>>> Coverage
mean coverageData = 0.017X
std coverageData = 0.1841X
There is a 1.55% of reference with a coverageData >= 1X
There is a 0.11% 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 5243950 0.021038864332458374 0.3205504645849755
chr2 243199373 4676171 0.019227726380692603 0.21968403573266926
chr3 198022430 3292789 0.01662836376667027 0.1398295584207576
chr4 191154276 2432625 0.012725977419411743 0.14256185953582376
chr5 180915260 3197624 0.017674705826363126 0.14266151450893244
chr6 171115067 3351889 0.019588508824883315 0.15629007227638902
chr7 159138663 3291283 0.020681856551729355 0.21281618909361708
chr8 146364022 4750461 0.03245648032273942 0.24493527228523482
chr9 141213431 1901922 0.013468421427987256 0.14874635685563622
chr10 135534747 2293079 0.01691875368314223 0.19805624458992974
chr11 135006516 2668355 0.019764638619368564 0.1689352961290076
chr12 133851895 1733533 0.012951127811825152 0.1246042065394463
chr13 115169878 1274323 0.011064724753811062 0.11344322714601185
chr14 107349540 972919 0.009063094261978207 0.1049471122437773
chr15 102531392 1360961 0.013273603073681082 0.12508128005553504
chr16 90354753 1598545 0.017691875047237415 0.14931030023031197
chr17 81195210 1190840 0.014666382413445325 0.13445075152998326
chr18 78077248 1383859 0.017724228702323114 0.22065036520831438
chr19 59128983 1111540 0.018798564487402056 0.21981357330583182
chr20 63025520 1017676 0.016147046466256844 0.14018544691628163
chr21 48129895 475811 0.009885976273166605 0.12868481135000995
chr22 51304566 990229 0.019300991650528728 0.1503754840743551
chrMT 16571 5508 0.33238790658379097 0.6733460711545171
chrX 155270560 2367136 0.015245233867901295 0.14088668619549227
chrY 59373566 168882 0.002844397117734178 0.1171510076234865