BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR960901.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 = 108,027,796
number of mapped reads = 106,447,005 (98.54%)
number of supplementary alignments = 260,054 (0.24%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 53,300,624
number of mapped paired reads (second in pair) = 53,146,381
number of mapped paired reads (both in pair) = 106,026,844
number of mapped paired reads (singletons) = 420,161
number of mapped bases = 10,511,377,472 bp
number of sequenced bases = 10,508,140,824 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,926,466
duplication rate = 4.27%
>>>>>>> Insert size
mean insert size = 23,111.0033
std insert size = 1,427,905.0201
median insert size = 148
>>>>>>> Mapping quality
mean mapping quality = 53.6339
>>>>>>> ACTG content
number of A's = 3,105,042,088 bp (29.55%)
number of C's = 2,143,870,153 bp (20.4%)
number of T's = 3,090,547,154 bp (29.41%)
number of G's = 2,168,410,579 bp (20.64%)
number of N's = 270,850 bp (0%)
GC percentage = 41.04%
>>>>>>> Mismatches and indels
general error rate = 0.0068
number of mismatches = 68,223,105
number of insertions = 1,156,257
mapped reads with insertion percentage = 1.05%
number of deletions = 1,273,277
mapped reads with deletion percentage = 1.16%
homopolymer indels = 41.53%
>>>>>>> Coverage
mean coverageData = 3.3955X
std coverageData = 37.3219X
There is a 84% of reference with a coverageData >= 1X
There is a 72.34% of reference with a coverageData >= 2X
There is a 56.56% of reference with a coverageData >= 3X
There is a 41.23% of reference with a coverageData >= 4X
There is a 27.77% of reference with a coverageData >= 5X
There is a 17.63% of reference with a coverageData >= 6X
There is a 10.56% of reference with a coverageData >= 7X
There is a 6.05% of reference with a coverageData >= 8X
There is a 3.35% of reference with a coverageData >= 9X
There is a 1.83% of reference with a coverageData >= 10X
There is a 1.01% of reference with a coverageData >= 11X
There is a 0.58% of reference with a coverageData >= 12X
There is a 0.36% of reference with a coverageData >= 13X
There is a 0.24% of reference with a coverageData >= 14X
There is a 0.18% of reference with a coverageData >= 15X
There is a 0.15% of reference with a coverageData >= 16X
There is a 0.13% of reference with a coverageData >= 17X
There is a 0.11% of reference with a coverageData >= 18X
There is a 0.1% of reference with a coverageData >= 19X
There is a 0.1% of reference with a coverageData >= 20X
There is a 0.09% of reference with a coverageData >= 21X
There is a 0.08% of reference with a coverageData >= 22X
There is a 0.08% of reference with a coverageData >= 23X
There is a 0.07% of reference with a coverageData >= 24X
There is a 0.07% of reference with a coverageData >= 25X
There is a 0.06% of reference with a coverageData >= 26X
There is a 0.06% of reference with a coverageData >= 27X
There is a 0.06% of reference with a coverageData >= 28X
There is a 0.05% of reference with a coverageData >= 29X
There is a 0.05% of reference with a coverageData >= 30X
There is a 0.05% of reference with a coverageData >= 31X
There is a 0.05% of reference with a coverageData >= 32X
There is a 0.05% of reference with a coverageData >= 33X
There is a 0.04% of reference with a coverageData >= 34X
There is a 0.04% of reference with a coverageData >= 35X
There is a 0.04% of reference with a coverageData >= 36X
There is a 0.04% of reference with a coverageData >= 37X
There is a 0.04% of reference with a coverageData >= 38X
There is a 0.04% of reference with a coverageData >= 39X
There is a 0.04% of reference with a coverageData >= 40X
There is a 0.03% of reference with a coverageData >= 41X
There is a 0.03% of reference with a coverageData >= 42X
There is a 0.03% of reference with a coverageData >= 43X
There is a 0.03% of reference with a coverageData >= 44X
There is a 0.03% of reference with a coverageData >= 45X
There is a 0.03% of reference with a coverageData >= 46X
There is a 0.03% of reference with a coverageData >= 47X
There is a 0.03% of reference with a coverageData >= 48X
There is a 0.03% of reference with a coverageData >= 49X
There is a 0.03% of reference with a coverageData >= 50X
There is a 0.03% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 855019943 3.4303623379939343 89.65040426467246
chr2 243199373 902146398 3.7094931079448137 23.50561734518468
chr3 198022430 693607468 3.5026712276988015 7.590490965803316
chr4 191154276 709875106 3.7136239944744944 32.277535548371
chr5 180915260 632720984 3.497333414549994 4.0887239753431714
chr6 171115067 602253639 3.5195827553864674 10.974394803922316
chr7 159138663 560960203 3.5249774782888554 22.870508178780764
chr8 146364022 529434940 3.6172478233756107 38.25138808431165
chr9 141213431 438456581 3.104921237980543 32.340184567204844
chr10 135534747 547860488 4.042214267017446 85.26647489530288
chr11 135006516 472790661 3.5019840153493034 14.953111034873627
chr12 133851895 463639081 3.463821569354696 5.570803944614431
chr13 115169878 335356414 2.911841358380183 2.6923645128768134
chr14 107349540 309692126 2.884894765268673 3.6370909241872393
chr15 102531392 291046782 2.8386114371684332 2.730550778336412
chr16 90354753 333836231 3.6947279464091944 34.8222245566126
chr17 81195210 278188149 3.4261645360606865 14.261112752764545
chr18 78077248 287246375 3.6790023003884564 38.598929558927686
chr19 59128983 201291248 3.404273805960776 43.36271017779701
chr20 63025520 215611866 3.421024784880791 12.57401838246012
chr21 48129895 144085292 2.9936755939317963 16.189786994093804
chr22 51304566 121669484 2.371513755715232 3.2404645987064313
chrMT 16571 8129756 490.6014121054855 76.25149660732154
chrX 155270560 541485776 3.487369247589498 11.520215957521808
chrY 59373566 34972481 0.5890244321858653 34.40731401778245