BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5038494.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,854,548
number of mapped reads = 11,047,682 (93.19%)
number of supplementary alignments = 206,764 (1.74%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 5,588,910
number of mapped paired reads (second in pair) = 5,458,772
number of mapped paired reads (both in pair) = 10,897,614
number of mapped paired reads (singletons) = 150,068
number of mapped bases = 1,571,577,467 bp
number of sequenced bases = 1,570,406,477 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,518,775
duplication rate = 8.75%
>>>>>>> Insert size
mean insert size = 94,575.466
std insert size = 2,937,131.6419
median insert size = 263
>>>>>>> Mapping quality
mean mapping quality = 53.7353
>>>>>>> ACTG content
number of A's = 454,709,616 bp (28.95%)
number of C's = 322,480,868 bp (20.53%)
number of T's = 455,547,677 bp (29.01%)
number of G's = 337,635,226 bp (21.5%)
number of N's = 33,090 bp (0%)
GC percentage = 42.03%
>>>>>>> Mismatches and indels
general error rate = 0.0139
number of mismatches = 21,059,739
number of insertions = 288,827
mapped reads with insertion percentage = 2.43%
number of deletions = 560,591
mapped reads with deletion percentage = 4.85%
homopolymer indels = 46.37%
>>>>>>> Coverage
mean coverageData = 0.5077X
std coverageData = 6.6329X
There is a 22.44% of reference with a coverageData >= 1X
There is a 11.42% of reference with a coverageData >= 2X
There is a 5.75% of reference with a coverageData >= 3X
There is a 3.23% of reference with a coverageData >= 4X
There is a 1.8% of reference with a coverageData >= 5X
There is a 1.06% of reference with a coverageData >= 6X
There is a 0.63% of reference with a coverageData >= 7X
There is a 0.39% of reference with a coverageData >= 8X
There is a 0.25% of reference with a coverageData >= 9X
There is a 0.16% of reference with a coverageData >= 10X
There is a 0.11% of reference with a coverageData >= 11X
There is a 0.08% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.02% of reference with a coverageData >= 23X
There is a 0.02% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 123829338 0.4968065375451963 5.6179340330583765
chr2 243199373 145221683 0.5971301702327991 7.9248504564329325
chr3 198022430 106834684 0.539507994119656 1.3230693525442314
chr4 191154276 105217517 0.5504324527901222 5.699620778950994
chr5 180915260 96463097 0.5331949167803756 1.3619038111481576
chr6 171115067 94132514 0.5501123638633177 6.9906299845021085
chr7 159138663 82112792 0.5159826685234876 6.052198532835152
chr8 146364022 80309414 0.5486964139315603 1.945799777816758
chr9 141213431 68032979 0.4817741380421527 11.482708127009596
chr10 135534747 88000614 0.6492845262772358 16.906543928800144
chr11 135006516 73197214 0.5421754161850973 3.552657177418488
chr12 133851895 67663153 0.5055076209417879 1.267547943439078
chr13 115169878 48507420 0.42118148288739177 1.1100754766065455
chr14 107349540 46050992 0.4289817357391564 1.2530386417566963
chr15 102531392 43669525 0.4259137045559666 1.1422681346141739
chr16 90354753 58338280 0.6456581204975459 12.488927097085744
chr17 81195210 36842641 0.45375387291935076 4.397682206146807
chr18 78077248 45673667 0.5849804926526099 10.111937135910932
chr19 59128983 20605308 0.34848067655755216 3.1002615874865667
chr20 63025520 32724076 0.5192194526915447 1.9574726199563042
chr21 48129895 20340330 0.42261322199019963 2.8889620665982947
chr22 51304566 15173750 0.29575827617370354 1.0951704889047595
chrMT 16571 2521584 152.1684871160461 66.71557952750737
chrX 155270560 48402347 0.31172906827926683 1.3592402714885405
chrY 59373566 21712548 0.36569385103128216 10.063853544474785