BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR960921.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 = 228,796,776
number of mapped reads = 223,960,439 (97.89%)
number of supplementary alignments = 462,616 (0.2%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 112,481,271
number of mapped paired reads (second in pair) = 111,479,168
number of mapped paired reads (both in pair) = 221,950,264
number of mapped paired reads (singletons) = 2,010,175
number of mapped bases = 21,839,608,087 bp
number of sequenced bases = 21,833,303,424 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 37,938,690
duplication rate = 12.18%
>>>>>>> Insert size
mean insert size = 18,993.3602
std insert size = 1,278,761.04
median insert size = 183
>>>>>>> Mapping quality
mean mapping quality = 53.5665
>>>>>>> ACTG content
number of A's = 6,687,775,074 bp (30.63%)
number of C's = 4,240,038,224 bp (19.42%)
number of T's = 6,686,034,067 bp (30.62%)
number of G's = 4,217,518,770 bp (19.32%)
number of N's = 1,937,289 bp (0.01%)
GC percentage = 38.74%
>>>>>>> Mismatches and indels
general error rate = 0.0149
number of mismatches = 319,248,044
number of insertions = 2,653,208
mapped reads with insertion percentage = 1.16%
number of deletions = 2,922,453
mapped reads with deletion percentage = 1.27%
homopolymer indels = 40.15%
>>>>>>> Coverage
mean coverageData = 7.0548X
std coverageData = 104.3531X
There is a 89.46% of reference with a coverageData >= 1X
There is a 85.27% of reference with a coverageData >= 2X
There is a 79.11% of reference with a coverageData >= 3X
There is a 71.46% of reference with a coverageData >= 4X
There is a 62.91% of reference with a coverageData >= 5X
There is a 54.07% of reference with a coverageData >= 6X
There is a 45.48% of reference with a coverageData >= 7X
There is a 37.52% of reference with a coverageData >= 8X
There is a 30.41% of reference with a coverageData >= 9X
There is a 24.28% of reference with a coverageData >= 10X
There is a 19.14% of reference with a coverageData >= 11X
There is a 14.93% of reference with a coverageData >= 12X
There is a 11.54% of reference with a coverageData >= 13X
There is a 8.86% of reference with a coverageData >= 14X
There is a 6.78% of reference with a coverageData >= 15X
There is a 5.17% of reference with a coverageData >= 16X
There is a 3.94% of reference with a coverageData >= 17X
There is a 3.01% of reference with a coverageData >= 18X
There is a 2.31% of reference with a coverageData >= 19X
There is a 1.78% of reference with a coverageData >= 20X
There is a 1.39% of reference with a coverageData >= 21X
There is a 1.09% of reference with a coverageData >= 22X
There is a 0.87% of reference with a coverageData >= 23X
There is a 0.71% of reference with a coverageData >= 24X
There is a 0.59% of reference with a coverageData >= 25X
There is a 0.5% of reference with a coverageData >= 26X
There is a 0.43% of reference with a coverageData >= 27X
There is a 0.38% of reference with a coverageData >= 28X
There is a 0.34% of reference with a coverageData >= 29X
There is a 0.31% of reference with a coverageData >= 30X
There is a 0.29% of reference with a coverageData >= 31X
There is a 0.27% of reference with a coverageData >= 32X
There is a 0.26% of reference with a coverageData >= 33X
There is a 0.24% of reference with a coverageData >= 34X
There is a 0.23% of reference with a coverageData >= 35X
There is a 0.22% of reference with a coverageData >= 36X
There is a 0.21% of reference with a coverageData >= 37X
There is a 0.2% of reference with a coverageData >= 38X
There is a 0.2% of reference with a coverageData >= 39X
There is a 0.19% of reference with a coverageData >= 40X
There is a 0.18% of reference with a coverageData >= 41X
There is a 0.17% of reference with a coverageData >= 42X
There is a 0.17% of reference with a coverageData >= 43X
There is a 0.16% of reference with a coverageData >= 44X
There is a 0.15% of reference with a coverageData >= 45X
There is a 0.15% of reference with a coverageData >= 46X
There is a 0.14% of reference with a coverageData >= 47X
There is a 0.14% of reference with a coverageData >= 48X
There is a 0.13% of reference with a coverageData >= 49X
There is a 0.13% of reference with a coverageData >= 50X
There is a 0.12% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1812775361 7.272902084364316 276.70792552289606
chr2 243199373 1839847835 7.5651832992184564 55.432556604158094
chr3 198022430 1625989396 8.211137475688991 9.630913024400476
chr4 191154276 1443573233 7.551875182745062 56.15616970446086
chr5 180915260 1188078727 6.567045405677774 9.45638493631816
chr6 171115067 1149143751 6.715619910898904 27.312769007410306
chr7 159138663 1201505326 7.550052912031817 69.09987773453227
chr8 146364022 1281979072 8.758840147205028 134.41091393619604
chr9 141213431 932171865 6.60115584189722 98.39321504228091
chr10 135534747 1039357184 7.6685662312115435 199.32764216203785
chr11 135006516 1064395031 7.884027101328946 43.53665337794396
chr12 133851895 988086947 7.381942160774041 11.702120685552497
chr13 115169878 755101413 6.5564141085571 4.893116589439207
chr14 107349540 464966176 4.331329002434477 7.45911421262948
chr15 102531392 587404369 5.729019742558455 5.183373691539303
chr16 90354753 715513795 7.918939195152246 86.03808463072274
chr17 81195210 414826357 5.109000358518686 25.83305828505624
chr18 78077248 839146018 10.747638262045301 101.183436035689
chr19 59128983 401959369 6.79800917597382 116.20075510638566
chr20 63025520 408929692 6.488319207838349 18.704776562225387
chr21 48129895 291444561 6.055374959783311 22.618550624916946
chr22 51304566 223463841 4.3556326156233345 5.704457999089002
chrMT 16571 4917358 296.74479512401183 57.094326983480876
chrX 155270560 1105448957 7.119501320791269 29.35403577351835
chrY 59373566 59582453 1.0035181818117511 52.15942686065633