BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1163151.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 78,902,294
number of mapped reads = 78,187,071 (99.09%)
number of supplementary alignments = 386,781 (0.49%)
number of secondary alignments = 0
number of mapped bases = 7,709,876,350 bp
number of sequenced bases = 7,708,930,249 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 40,833,102
duplication rate = 41.52%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.385
>>>>>>> ACTG content
number of A's = 1,884,344,831 bp (24.44%)
number of C's = 1,971,290,127 bp (25.57%)
number of T's = 1,888,377,786 bp (24.5%)
number of G's = 1,964,662,729 bp (25.49%)
number of N's = 254,776 bp (0%)
GC percentage = 51.06%
>>>>>>> Mismatches and indels
general error rate = 0.0032
number of mismatches = 23,550,250
number of insertions = 557,288
mapped reads with insertion percentage = 0.7%
number of deletions = 388,673
mapped reads with deletion percentage = 0.49%
homopolymer indels = 45.93%
>>>>>>> Coverage
mean coverageData = 2.4905X
std coverageData = 28.8746X
There is a 10% of reference with a coverageData >= 1X
There is a 6.43% of reference with a coverageData >= 2X
There is a 4.91% of reference with a coverageData >= 3X
There is a 4.36% of reference with a coverageData >= 4X
There is a 3.97% of reference with a coverageData >= 5X
There is a 3.7% of reference with a coverageData >= 6X
There is a 3.49% of reference with a coverageData >= 7X
There is a 3.31% of reference with a coverageData >= 8X
There is a 3.16% of reference with a coverageData >= 9X
There is a 3.02% of reference with a coverageData >= 10X
There is a 2.9% of reference with a coverageData >= 11X
There is a 2.79% of reference with a coverageData >= 12X
There is a 2.69% of reference with a coverageData >= 13X
There is a 2.6% of reference with a coverageData >= 14X
There is a 2.51% of reference with a coverageData >= 15X
There is a 2.43% of reference with a coverageData >= 16X
There is a 2.36% of reference with a coverageData >= 17X
There is a 2.29% of reference with a coverageData >= 18X
There is a 2.23% of reference with a coverageData >= 19X
There is a 2.17% of reference with a coverageData >= 20X
There is a 2.11% of reference with a coverageData >= 21X
There is a 2.05% of reference with a coverageData >= 22X
There is a 2% of reference with a coverageData >= 23X
There is a 1.95% of reference with a coverageData >= 24X
There is a 1.9% of reference with a coverageData >= 25X
There is a 1.86% of reference with a coverageData >= 26X
There is a 1.82% of reference with a coverageData >= 27X
There is a 1.77% of reference with a coverageData >= 28X
There is a 1.73% of reference with a coverageData >= 29X
There is a 1.7% of reference with a coverageData >= 30X
There is a 1.66% of reference with a coverageData >= 31X
There is a 1.62% of reference with a coverageData >= 32X
There is a 1.59% of reference with a coverageData >= 33X
There is a 1.56% of reference with a coverageData >= 34X
There is a 1.53% of reference with a coverageData >= 35X
There is a 1.5% of reference with a coverageData >= 36X
There is a 1.47% of reference with a coverageData >= 37X
There is a 1.44% of reference with a coverageData >= 38X
There is a 1.41% of reference with a coverageData >= 39X
There is a 1.38% of reference with a coverageData >= 40X
There is a 1.36% of reference with a coverageData >= 41X
There is a 1.33% of reference with a coverageData >= 42X
There is a 1.31% of reference with a coverageData >= 43X
There is a 1.29% of reference with a coverageData >= 44X
There is a 1.26% of reference with a coverageData >= 45X
There is a 1.24% of reference with a coverageData >= 46X
There is a 1.22% of reference with a coverageData >= 47X
There is a 1.2% of reference with a coverageData >= 48X
There is a 1.18% of reference with a coverageData >= 49X
There is a 1.16% of reference with a coverageData >= 50X
There is a 1.14% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 855500304 3.4322895588693436 33.44975502946257
chr2 243199373 503581503 2.0706529658692827 22.30380126129319
chr3 198022430 382048474 1.9293191887403867 21.41835071275804
chr4 191154276 264018247 1.3811788704114576 17.73737907027021
chr5 180915260 384066967 2.1229108423468532 31.917512647482745
chr6 171115067 394048562 2.302827967802508 27.66444164651051
chr7 159138663 426775677 2.6817849852112934 33.9397935151292
chr8 146364022 349407285 2.38724845235532 40.097327094549435
chr9 141213431 344984990 2.4430040935695416 28.075090240018955
chr10 135534747 300859613 2.219796913038101 25.64048352201645
chr11 135006516 396316529 2.9355363040403177 28.59360638654647
chr12 133851895 367940765 2.748864818088679 28.41888503015781
chr13 115169878 129760690 1.1266894803865295 14.030319391781227
chr14 107349540 195535577 1.821485001239875 20.267226027377806
chr15 102531392 324986075 3.169625113448182 35.93336317073721
chr16 90354753 282998652 3.1320837322193777 26.877933623473208
chr17 81195210 391695577 4.824121730826239 37.68009649064862
chr18 78077248 129207143 1.6548629249842413 23.025598543397784
chr19 59128983 430425919 7.279440591765294 50.62871739656699
chr20 63025520 174312994 2.765752571339356 28.3313170588909
chr21 48129895 91155726 1.893952313837377 29.226893364588246
chr22 51304566 145695971 2.8398246464067154 25.249583714054374
chrMT 16571 910 0.05491521332448253 0.3036843357379764
chrX 155270560 437708305 2.8190038407796045 33.538195929872295
chrY 59373566 6843895 0.11526838391347421 6.388019008550628