BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1819097.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 5,206,067
number of mapped reads = 4,775,836 (91.74%)
number of supplementary alignments = 18,762 (0.36%)
number of secondary alignments = 0
number of mapped bases = 278,938,118 bp
number of sequenced bases = 278,853,389 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 386,862
duplication rate = 5.87%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0576
>>>>>>> ACTG content
number of A's = 66,854,802 bp (23.97%)
number of C's = 50,019,898 bp (17.94%)
number of T's = 91,575,584 bp (32.84%)
number of G's = 70,399,254 bp (25.25%)
number of N's = 3,851 bp (0%)
GC percentage = 43.18%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 1,393,243
number of insertions = 15,127
mapped reads with insertion percentage = 0.32%
number of deletions = 50,620
mapped reads with deletion percentage = 1.05%
homopolymer indels = 45.77%
>>>>>>> Coverage
mean coverageData = 0.0901X
std coverageData = 0.7387X
There is a 6.92% of reference with a coverageData >= 1X
There is a 1.38% of reference with a coverageData >= 2X
There is a 0.34% of reference with a coverageData >= 3X
There is a 0.1% of reference with a coverageData >= 4X
There is a 0.04% 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 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% 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 27658013 0.11096467037488345 1.562570255536558
chr2 243199373 22344182 0.09187598522303757 0.8385626742449943
chr3 198022430 15085276 0.07617963278200353 0.3556557758530975
chr4 191154276 15699458 0.08212977668362491 0.469292606216324
chr5 180915260 15551428 0.0859597360664877 0.3751201336880289
chr6 171115067 12010113 0.07018734942844046 0.5201581656603302
chr7 159138663 14001383 0.08798228372699098 0.976777565515975
chr8 146364022 25374814 0.1733678376233744 0.7277238466117898
chr9 141213431 12210058 0.08646527397241698 0.5897048279459248
chr10 135534747 14803032 0.10921946089588377 0.7623456672784943
chr11 135006516 9633700 0.07135729656189335 0.674680887342006
chr12 133851895 12943452 0.09669980391387062 0.39855739116744987
chr13 115169878 6118377 0.05312480230290771 0.2885705312897097
chr14 107349540 6698686 0.06240069589492419 0.3310093169934229
chr15 102531392 7488733 0.07303844075383274 0.358630251907096
chr16 90354753 8663385 0.09588189566518986 0.4625172637640685
chr17 81195210 9571130 0.11787801275469328 0.49583448991568424
chr18 78077248 6613821 0.08470868491676346 1.2306175980625844
chr19 59128983 5717758 0.09669975213339962 1.0196383592137588
chr20 63025520 7634962 0.12114080137696603 0.4511103169825248
chr21 48129895 3746527 0.07784199404548878 0.43243141891730497
chr22 51304566 2380850 0.046406200960748795 0.26886168439933733
chrMT 16571 19709 1.1893669663870616 1.52217224369425
chrX 155270560 16046374 0.1033446005475861 0.5014021924108238
chrY 59373566 922897 0.015543903830873153 0.42254051485496824