BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8438269.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 755,054,160
number of mapped reads = 752,629,046 (99.68%)
number of supplementary alignments = 12,421,233 (1.65%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 376,558,952
number of mapped paired reads (second in pair) = 376,070,094
number of mapped paired reads (both in pair) = 750,937,080
number of mapped paired reads (singletons) = 1,691,966
number of mapped bases = 107,849,957,044 bp
number of sequenced bases = 107,821,507,571 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 292,804,408
duplication rate = 35.93%
>>>>>>> Insert size
mean insert size = 43,649.6418
std insert size = 2,073,739.7367
median insert size = 255
>>>>>>> Mapping quality
mean mapping quality = 55.1055
>>>>>>> ACTG content
number of A's = 32,562,119,319 bp (30.2%)
number of C's = 21,609,064,409 bp (20.04%)
number of T's = 31,055,253,724 bp (28.8%)
number of G's = 22,594,261,173 bp (20.96%)
number of N's = 808,946 bp (0%)
GC percentage = 41%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 553,539,141
number of insertions = 13,078,178
mapped reads with insertion percentage = 1.71%
number of deletions = 11,531,704
mapped reads with deletion percentage = 1.51%
homopolymer indels = 48.41%
>>>>>>> Coverage
mean coverageData = 34.8387X
std coverageData = 93.2989X
There is a 91.48% of reference with a coverageData >= 1X
There is a 90.85% of reference with a coverageData >= 2X
There is a 90.12% of reference with a coverageData >= 3X
There is a 89.31% of reference with a coverageData >= 4X
There is a 88.4% of reference with a coverageData >= 5X
There is a 87.41% of reference with a coverageData >= 6X
There is a 86.31% of reference with a coverageData >= 7X
There is a 85.13% of reference with a coverageData >= 8X
There is a 83.86% of reference with a coverageData >= 9X
There is a 82.5% of reference with a coverageData >= 10X
There is a 81.08% of reference with a coverageData >= 11X
There is a 79.59% of reference with a coverageData >= 12X
There is a 78.04% of reference with a coverageData >= 13X
There is a 76.44% of reference with a coverageData >= 14X
There is a 74.79% of reference with a coverageData >= 15X
There is a 73.11% of reference with a coverageData >= 16X
There is a 71.4% of reference with a coverageData >= 17X
There is a 69.67% of reference with a coverageData >= 18X
There is a 67.92% of reference with a coverageData >= 19X
There is a 66.15% of reference with a coverageData >= 20X
There is a 64.39% of reference with a coverageData >= 21X
There is a 62.62% of reference with a coverageData >= 22X
There is a 60.85% of reference with a coverageData >= 23X
There is a 59.1% of reference with a coverageData >= 24X
There is a 57.35% of reference with a coverageData >= 25X
There is a 55.63% of reference with a coverageData >= 26X
There is a 53.92% of reference with a coverageData >= 27X
There is a 52.24% of reference with a coverageData >= 28X
There is a 50.58% of reference with a coverageData >= 29X
There is a 48.95% of reference with a coverageData >= 30X
There is a 47.35% of reference with a coverageData >= 31X
There is a 45.78% of reference with a coverageData >= 32X
There is a 44.25% of reference with a coverageData >= 33X
There is a 42.74% of reference with a coverageData >= 34X
There is a 41.28% of reference with a coverageData >= 35X
There is a 39.84% of reference with a coverageData >= 36X
There is a 38.45% of reference with a coverageData >= 37X
There is a 37.09% of reference with a coverageData >= 38X
There is a 35.77% of reference with a coverageData >= 39X
There is a 34.49% of reference with a coverageData >= 40X
There is a 33.24% of reference with a coverageData >= 41X
There is a 32.03% of reference with a coverageData >= 42X
There is a 30.86% of reference with a coverageData >= 43X
There is a 29.72% of reference with a coverageData >= 44X
There is a 28.62% of reference with a coverageData >= 45X
There is a 27.55% of reference with a coverageData >= 46X
There is a 26.52% of reference with a coverageData >= 47X
There is a 25.53% of reference with a coverageData >= 48X
There is a 24.56% of reference with a coverageData >= 49X
There is a 23.63% of reference with a coverageData >= 50X
There is a 22.73% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 9474549543 38.01214017035488 33.70380590302579
chr2 243199373 9837030704 40.4484213205599 151.37116340237853
chr3 198022430 7257111275 36.647925565805856 148.98205511651435
chr4 191154276 7193158287 37.63011969975498 30.21205566261987
chr5 180915260 7019570010 38.800320160941645 32.33421406802148
chr6 171115067 6575510063 38.4274171660173 30.16762271959641
chr7 159138663 5975021159 37.54600576856675 30.155906022966434
chr8 146364022 5915356618 40.41537351303451 30.813529109932016
chr9 141213431 4714556058 33.38603151707291 34.1351736746698
chr10 135534747 5351267599 39.48262506440507 37.77359153630624
chr11 135006516 4936124178 36.562118068434565 28.881445486011906
chr12 133851895 4977544029 37.18695225794151 28.54596406899711
chr13 115169878 3798018440 32.977532892758646 29.19101043906618
chr14 107349540 3383622379 31.51967282766186 30.356581274983284
chr15 102531392 2828944150 27.591005006544727 28.1657009228212
chr16 90354753 2607554432 28.85907321333721 43.00845912906005
chr17 81195210 2446138958 30.126641189794324 33.123767781112626
chr18 78077248 3195061850 40.92180413428506 31.455530539829557
chr19 59128983 1574919022 26.635313886592638 181.29477086414747
chr20 63025520 2204538637 34.97850770608477 29.453293967533387
chr21 48129895 1405695667 29.206289916069835 90.54555619212003
chr22 51304566 1209859450 23.581905945759292 30.001575059778
chrMT 16571 417355456 25185.89439382053 9431.55968791371
chrX 155270560 3140742279 20.227545253910336 31.282051594496703
chrY 59373566 410706801 6.9173342392808275 19.415033813058017