BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524964.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 = 1,056,297
number of mapped reads = 981,824 (92.95%)
number of supplementary alignments = 2,617 (0.25%)
number of secondary alignments = 0
number of mapped bases = 57,572,281 bp
number of sequenced bases = 57,553,046 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 22,946
duplication rate = 1.63%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.5064
>>>>>>> ACTG content
number of A's = 14,424,242 bp (25.06%)
number of C's = 10,718,788 bp (18.62%)
number of T's = 18,341,596 bp (31.87%)
number of G's = 14,067,724 bp (24.44%)
number of N's = 696 bp (0%)
GC percentage = 43.07%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 279,933
number of insertions = 3,681
mapped reads with insertion percentage = 0.37%
number of deletions = 11,119
mapped reads with deletion percentage = 1.12%
homopolymer indels = 41.95%
>>>>>>> Coverage
mean coverageData = 0.0186X
std coverageData = 0.191X
There is a 1.73% of reference with a coverageData >= 1X
There is a 0.09% 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 6072832 0.0243643605606102 0.3374256140845731
chr2 243199373 5086823 0.0209162669181717 0.21387533294963726
chr3 198022430 3181399 0.016065851732048737 0.13488753469159173
chr4 191154276 3719656 0.019458921232816156 0.1538325003362442
chr5 180915260 2490953 0.013768617417900513 0.12472693768577953
chr6 171115067 3860609 0.022561479054325474 0.20002169746092638
chr7 159138663 3676525 0.023102651050926574 0.25729466552632246
chr8 146364022 3490892 0.02385075206528555 0.19486183795965914
chr9 141213431 1595478 0.011298344560440573 0.14745325284745614
chr10 135534747 2920262 0.02154622386243138 0.1914777047586311
chr11 135006516 2414763 0.017886270022700237 0.17282242245528517
chr12 133851895 3167762 0.023666172227147026 0.16273107925642002
chr13 115169878 1649265 0.014320280863716813 0.12727530833932288
chr14 107349540 1299589 0.012106144097124218 0.11779735849573969
chr15 102531392 1597298 0.015578623959382119 0.13912323083807612
chr16 90354753 1814393 0.020080769851697784 0.15471109076335013
chr17 81195210 1478758 0.01821237976969331 0.17698468433404468
chr18 78077248 1135323 0.014541022245046342 0.22200997646157458
chr19 59128983 1374351 0.023243271408879128 0.2233381840537825
chr20 63025520 1394334 0.02212332401224139 0.15820521549964972
chr21 48129895 844188 0.017539784784487894 0.14238913045399296
chr22 51304566 730666 0.014241734351675443 0.12430348339116541
chrMT 16571 4254 0.25671353569488864 0.556826866723216
chrX 155270560 2423056 0.015605379409979586 0.14716127021880607
chrY 59373566 148852 0.0025070416016447455 0.06892118573621725