BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8438283.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 = 817,262,372
number of mapped reads = 814,634,826 (99.68%)
number of supplementary alignments = 13,114,161 (1.6%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 407,532,973
number of mapped paired reads (second in pair) = 407,101,853
number of mapped paired reads (both in pair) = 812,791,418
number of mapped paired reads (singletons) = 1,843,408
number of mapped bases = 117,134,569,327 bp
number of sequenced bases = 117,102,187,535 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 371,245,518
duplication rate = 42.86%
>>>>>>> Insert size
mean insert size = 42,308.7194
std insert size = 2,018,918.2095
median insert size = 240
>>>>>>> Mapping quality
mean mapping quality = 55.1356
>>>>>>> ACTG content
number of A's = 35,416,120,324 bp (30.24%)
number of C's = 23,401,884,939 bp (19.98%)
number of T's = 33,803,569,130 bp (28.87%)
number of G's = 24,479,893,821 bp (20.9%)
number of N's = 719,321 bp (0%)
GC percentage = 40.89%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 605,841,587
number of insertions = 14,787,813
mapped reads with insertion percentage = 1.78%
number of deletions = 13,159,225
mapped reads with deletion percentage = 1.59%
homopolymer indels = 48.38%
>>>>>>> Coverage
mean coverageData = 37.8379X
std coverageData = 82.6456X
There is a 91.72% of reference with a coverageData >= 1X
There is a 91.24% of reference with a coverageData >= 2X
There is a 90.69% of reference with a coverageData >= 3X
There is a 90.11% of reference with a coverageData >= 4X
There is a 89.44% of reference with a coverageData >= 5X
There is a 88.72% of reference with a coverageData >= 6X
There is a 87.91% of reference with a coverageData >= 7X
There is a 87.03% of reference with a coverageData >= 8X
There is a 86.06% of reference with a coverageData >= 9X
There is a 85.02% of reference with a coverageData >= 10X
There is a 83.9% of reference with a coverageData >= 11X
There is a 82.71% of reference with a coverageData >= 12X
There is a 81.45% of reference with a coverageData >= 13X
There is a 80.12% of reference with a coverageData >= 14X
There is a 78.73% of reference with a coverageData >= 15X
There is a 77.29% of reference with a coverageData >= 16X
There is a 75.8% of reference with a coverageData >= 17X
There is a 74.26% of reference with a coverageData >= 18X
There is a 72.68% of reference with a coverageData >= 19X
There is a 71.07% of reference with a coverageData >= 20X
There is a 69.44% of reference with a coverageData >= 21X
There is a 67.78% of reference with a coverageData >= 22X
There is a 66.11% of reference with a coverageData >= 23X
There is a 64.43% of reference with a coverageData >= 24X
There is a 62.73% of reference with a coverageData >= 25X
There is a 61.04% of reference with a coverageData >= 26X
There is a 59.36% of reference with a coverageData >= 27X
There is a 57.68% of reference with a coverageData >= 28X
There is a 56.01% of reference with a coverageData >= 29X
There is a 54.35% of reference with a coverageData >= 30X
There is a 52.72% of reference with a coverageData >= 31X
There is a 51.1% of reference with a coverageData >= 32X
There is a 49.51% of reference with a coverageData >= 33X
There is a 47.94% of reference with a coverageData >= 34X
There is a 46.4% of reference with a coverageData >= 35X
There is a 44.89% of reference with a coverageData >= 36X
There is a 43.41% of reference with a coverageData >= 37X
There is a 41.96% of reference with a coverageData >= 38X
There is a 40.54% of reference with a coverageData >= 39X
There is a 39.16% of reference with a coverageData >= 40X
There is a 37.8% of reference with a coverageData >= 41X
There is a 36.49% of reference with a coverageData >= 42X
There is a 35.21% of reference with a coverageData >= 43X
There is a 33.96% of reference with a coverageData >= 44X
There is a 32.75% of reference with a coverageData >= 45X
There is a 31.57% of reference with a coverageData >= 46X
There is a 30.43% of reference with a coverageData >= 47X
There is a 29.32% of reference with a coverageData >= 48X
There is a 28.25% of reference with a coverageData >= 49X
There is a 27.21% of reference with a coverageData >= 50X
There is a 26.2% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 9583727762 38.45016603589525 35.70809080743861
chr2 243199373 10402048642 42.771691857939125 147.27690317952167
chr3 198022430 8424973298 42.54555051162639 28.631162690227335
chr4 191154276 7892020885 41.28613311794291 28.568775111863864
chr5 180915260 7644442683 42.25427243119237 28.923777424126737
chr6 171115067 7034509148 41.10981733712555 30.671510468923174
chr7 159138663 6349019241 39.89614542004792 29.34872490216527
chr8 146364022 6100051600 41.67726136960079 29.98132975646457
chr9 141213431 5065203119 35.869131449684836 37.3966621660144
chr10 135534747 5633523270 41.565158711662335 41.18381869250103
chr11 135006516 5624802104 41.66318982707472 31.10052312685808
chr12 133851895 5390721310 40.273776549820234 28.91700717838127
chr13 115169878 4007580964 34.79712780454626 29.82911690373307
chr14 107349540 3714985731 34.60644294330465 32.05476731964124
chr15 102531392 3434780162 33.49979060071671 32.817773566783586
chr16 90354753 3161493094 34.98978182143888 58.2065842531369
chr17 81195210 2829463218 34.84766180172451 41.269345182744566
chr18 78077248 3248915331 41.611550281587796 31.930874200567352
chr19 59128983 1781039646 30.121262968449837 31.413068256420207
chr20 63025520 2549605418 40.453540375390794 33.64645955304818
chr21 48129895 1491833263 30.995980003696246 35.965447907642115
chr22 51304566 1270478278 24.763454348293287 31.868995548232157
chrMT 16571 426106042 25713.96065415485 10216.816731896122
chrX 155270560 3481341394 22.42112989094649 17.890147723102636
chrY 59373566 591903724 9.969145595870055 31.34953938984386