BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR617381.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000
number of mapped reads = 29,655,623 (92.67%)
number of supplementary alignments = 65,035 (0.2%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 14,925,843
number of mapped paired reads (second in pair) = 14,729,780
number of mapped paired reads (both in pair) = 29,088,224
number of mapped paired reads (singletons) = 567,399
number of mapped bases = 2,906,001,740 bp
number of sequenced bases = 2,905,157,016 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,522,355
duplication rate = 1.47%
>>>>>>> Insert size
mean insert size = 47,084.7533
std insert size = 2,053,026.1125
median insert size = 207
>>>>>>> Mapping quality
mean mapping quality = 53.4009
>>>>>>> ACTG content
number of A's = 883,045,723 bp (30.4%)
number of C's = 574,600,904 bp (19.78%)
number of T's = 869,298,390 bp (29.92%)
number of G's = 576,961,833 bp (19.86%)
number of N's = 1,250,166 bp (0.04%)
GC percentage = 39.64%
>>>>>>> Mismatches and indels
general error rate = 0.0137
number of mismatches = 38,947,957
number of insertions = 292,145
mapped reads with insertion percentage = 0.95%
number of deletions = 352,544
mapped reads with deletion percentage = 1.15%
homopolymer indels = 40.89%
>>>>>>> Coverage
mean coverageData = 0.9387X
std coverageData = 9.6127X
There is a 52.15% of reference with a coverageData >= 1X
There is a 23.42% of reference with a coverageData >= 2X
There is a 8.98% of reference with a coverageData >= 3X
There is a 3.16% of reference with a coverageData >= 4X
There is a 1.09% of reference with a coverageData >= 5X
There is a 0.4% of reference with a coverageData >= 6X
There is a 0.18% of reference with a coverageData >= 7X
There is a 0.1% of reference with a coverageData >= 8X
There is a 0.07% of reference with a coverageData >= 9X
There is a 0.06% of reference with a coverageData >= 10X
There is a 0.05% of reference with a coverageData >= 11X
There is a 0.04% of reference with a coverageData >= 12X
There is a 0.04% of reference with a coverageData >= 13X
There is a 0.03% of reference with a coverageData >= 14X
There is a 0.03% 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 0.03% 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 0.02% of reference with a coverageData >= 30X
There is a 0.02% of reference with a coverageData >= 31X
There is a 0.02% of reference with a coverageData >= 32X
There is a 0.02% of reference with a coverageData >= 33X
There is a 0.02% of reference with a coverageData >= 34X
There is a 0.02% of reference with a coverageData >= 35X
There is a 0.02% 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 188508879 0.7563025449794165 19.71044180351576
chr2 243199373 286903009 1.1797029139544697 8.611476996964774
chr3 198022430 232047224 1.171822929351993 1.4708239260605203
chr4 191154276 159870659 0.8363436191194593 8.820261599766242
chr5 180915260 183370092 1.0135689604072093 1.455255913364205
chr6 171115067 136763789 0.7992504190177478 3.611699147166424
chr7 159138663 236360845 1.4852509160517453 10.832343028225118
chr8 146364022 122501584 0.8369651388781869 7.429626720141347
chr9 141213431 122428857 0.86697742653105 14.39553342734426
chr10 135534747 122292448 0.902295910878116 20.00366985559723
chr11 135006516 155833014 1.1542629097991093 5.392383658720287
chr12 133851895 128203043 0.9577977435433395 1.3258058199768257
chr13 115169878 127390276 1.106107588305338 1.2866370917034553
chr14 107349540 83967568 0.7821884285670903 1.3655664338285611
chr15 102531392 65145248 0.6353688049022098 0.9691149525560042
chr16 90354753 72477243 0.8021409012097017 7.915132709967592
chr17 81195210 89435680 1.1014896075766045 6.895590492403772
chr18 78077248 52437561 0.6716112868117483 14.760726732724407
chr19 59128983 52794884 0.8928765779719229 9.650003695725403
chr20 63025520 82554972 1.3098657813533312 2.465935244375641
chr21 48129895 46262724 0.9612055875043982 3.177746672334788
chr22 51304566 25260512 0.49236381806640755 0.8982304397003443
chrMT 16571 1929005 116.40848470219058 21.118824032314777
chrX 155270560 121568243 0.7829445775168197 2.929045283232381
chrY 59373566 9694381 0.1632777286781124 7.874361455212204