BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716586.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 = 5,027,790
number of mapped reads = 4,399,473 (87.5%)
number of supplementary alignments = 23,164 (0.46%)
number of secondary alignments = 0
number of mapped bases = 254,583,449 bp
number of sequenced bases = 254,515,716 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 288,579
duplication rate = 4.91%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.2196
>>>>>>> ACTG content
number of A's = 65,126,378 bp (25.59%)
number of C's = 50,748,796 bp (19.94%)
number of T's = 78,755,219 bp (30.94%)
number of G's = 59,881,739 bp (23.53%)
number of N's = 3,584 bp (0%)
GC percentage = 43.47%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 1,238,078
number of insertions = 20,056
mapped reads with insertion percentage = 0.45%
number of deletions = 43,794
mapped reads with deletion percentage = 0.99%
homopolymer indels = 39.86%
>>>>>>> Coverage
mean coverageData = 0.0822X
std coverageData = 0.6261X
There is a 6.49% of reference with a coverageData >= 1X
There is a 1.19% of reference with a coverageData >= 2X
There is a 0.27% of reference with a coverageData >= 3X
There is a 0.08% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% 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 28421285 0.11402693756979647 1.156895601258292
chr2 243199373 21240730 0.08733875313074924 0.8387973471267233
chr3 198022430 22620403 0.11423151912639391 0.42154015386160726
chr4 191154276 11724330 0.06133438521668226 0.3358236263046883
chr5 180915260 10960913 0.06058589529705786 0.30906658787438707
chr6 171115067 18532378 0.1083036013421308 0.9182820442450329
chr7 159138663 14324619 0.0900134431819375 0.7164463705809481
chr8 146364022 20494910 0.14002696646311072 0.5532801896403126
chr9 141213431 9450943 0.06692665798906905 0.5055500822331214
chr10 135534747 13600410 0.10034629717499675 0.646285147591707
chr11 135006516 8384945 0.062107705971762135 0.49452183735802274
chr12 133851895 11269161 0.08419126976125366 0.3701366034022885
chr13 115169878 5638602 0.04895899950506156 0.2721769954136232
chr14 107349540 5459767 0.050859714908885495 0.34127134261238157
chr15 102531392 7580158 0.07393011888495574 0.342789087978946
chr16 90354753 5332731 0.05901992781718965 0.3598086689011069
chr17 81195210 5576372 0.06867858337948754 0.3528189778962125
chr18 78077248 4858284 0.06222406814338538 0.983270522701077
chr19 59128983 4951849 0.08374656130987404 0.7872399564957723
chr20 63025520 3906074 0.06197606937634152 0.3126758177915748
chr21 48129895 2327827 0.04836551170535485 0.31296952467421185
chr22 51304566 4050961 0.07895907354522792 0.3470261672127995
chrMT 16571 4288 0.25876531289602317 0.554463259071873
chrX 155270560 13290016 0.08559263262784651 0.4530213677987371
chrY 59373566 581493 0.009793802851592238 0.18672068525724392