BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716881.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 = 456,084
number of mapped reads = 407,892 (89.43%)
number of supplementary alignments = 911 (0.2%)
number of secondary alignments = 0
number of mapped bases = 23,087,991 bp
number of sequenced bases = 23,081,288 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,203
duplication rate = 1.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.1809
>>>>>>> ACTG content
number of A's = 5,648,963 bp (24.47%)
number of C's = 4,386,829 bp (19.01%)
number of T's = 7,390,366 bp (32.02%)
number of G's = 5,654,982 bp (24.5%)
number of N's = 148 bp (0%)
GC percentage = 43.51%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 114,244
number of insertions = 1,365
mapped reads with insertion percentage = 0.33%
number of deletions = 4,193
mapped reads with deletion percentage = 1.02%
homopolymer indels = 44.19%
>>>>>>> Coverage
mean coverageData = 0.0075X
std coverageData = 0.0995X
There is a 0.71% of reference with a coverageData >= 1X
There is a 0.02% of reference with a coverageData >= 2X
There is a 0% 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 2728079 0.010945124184866123 0.1288852435310341
chr2 243199373 2311620 0.009505040952552127 0.12685306555166856
chr3 198022430 1444691 0.007295592726541129 0.0886443107924487
chr4 191154276 980195 0.005127769153330371 0.07499098374583325
chr5 180915260 1643917 0.009086668531996692 0.09819225438788912
chr6 171115067 875243 0.005114938242112835 0.0776361351788813
chr7 159138663 1589189 0.00998619047088513 0.13857072978748305
chr8 146364022 1035617 0.007075625456643983 0.09002291515401314
chr9 141213431 642112 0.004547102888534732 0.0759457946936172
chr10 135534747 1050239 0.00774885424768602 0.10836661578592656
chr11 135006516 962528 0.007129492920178756 0.09707913276145291
chr12 133851895 951918 0.007111725986397129 0.08690837238412985
chr13 115169878 672347 0.005837871947732722 0.07902393948021937
chr14 107349540 483093 0.004500186959347939 0.06955052094662524
chr15 102531392 997151 0.009725323928109745 0.10191027917940222
chr16 90354753 700128 0.007748657118237045 0.09374463959684134
chr17 81195210 875015 0.010776682516123796 0.10904126932166776
chr18 78077248 714710 0.009153883087682599 0.12790533951806454
chr19 59128983 376246 0.006363140052654042 0.09678435667068279
chr20 63025520 586057 0.009298725341734586 0.0994134897285444
chr21 48129895 299251 0.006217570181692688 0.08179543269925013
chr22 51304566 273359 0.005328161240073642 0.07505495370905445
chrMT 16571 697 0.0420614326232575 0.2007293414250559
chrX 155270560 841975 0.00542263130885855 0.08135303878727783
chrY 59373566 52614 8.861519282840447E-4 0.0341464522876612