BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1506339.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 = 7,705,953
number of mapped reads = 5,458,496 (70.83%)
number of supplementary alignments = 79,624 (1.03%)
number of secondary alignments = 0
number of mapped bases = 414,546,965 bp
number of sequenced bases = 414,378,484 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 834,772
duplication rate = 11.51%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.3935
>>>>>>> ACTG content
number of A's = 116,414,592 bp (28.09%)
number of C's = 76,814,513 bp (18.54%)
number of T's = 120,024,351 bp (28.96%)
number of G's = 101,019,466 bp (24.38%)
number of N's = 105,562 bp (0.03%)
GC percentage = 42.92%
>>>>>>> Mismatches and indels
general error rate = 0.0074
number of mismatches = 2,997,293
number of insertions = 33,509
mapped reads with insertion percentage = 0.6%
number of deletions = 85,799
mapped reads with deletion percentage = 1.54%
homopolymer indels = 44.73%
>>>>>>> Coverage
mean coverageData = 0.1339X
std coverageData = 0.9173X
There is a 7.81% of reference with a coverageData >= 1X
There is a 2.94% of reference with a coverageData >= 2X
There is a 1.22% of reference with a coverageData >= 3X
There is a 0.55% of reference with a coverageData >= 4X
There is a 0.27% of reference with a coverageData >= 5X
There is a 0.14% of reference with a coverageData >= 6X
There is a 0.08% of reference with a coverageData >= 7X
There is a 0.05% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% 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 31322550 0.12566688850897587 1.4653467352696614
chr2 243199373 33473835 0.13763947902941345 1.0153280430621856
chr3 198022430 27093067 0.13681817256762277 0.5893103310102753
chr4 191154276 25143198 0.13153353681714136 0.8248771509135844
chr5 180915260 29565759 0.16342324577816156 0.6387572639046968
chr6 171115067 15097935 0.08823264522930643 0.5153292878818628
chr7 159138663 21004372 0.1319878626855122 1.1082644691619583
chr8 146364022 26456192 0.18075611505127948 1.2390514230776013
chr9 141213431 11638851 0.08242028337941877 0.8659492901340927
chr10 135534747 22880674 0.16881777187365835 1.037261574120933
chr11 135006516 17214480 0.12750851225580845 0.8512778546373896
chr12 133851895 17999489 0.13447317275560425 0.6785717055753758
chr13 115169878 9029546 0.07840197590554016 0.43209594222424963
chr14 107349540 11913253 0.11097628364313439 0.6112999028849625
chr15 102531392 15461242 0.15079520231228305 0.6448542663249819
chr16 90354753 15407655 0.17052401216790444 0.8118219678412484
chr17 81195210 10915947 0.13444077550880157 0.6975190331976395
chr18 78077248 7707174 0.09871216260081297 1.4644166940601364
chr19 59128983 9827704 0.16620789841760006 1.1697204308189242
chr20 63025520 11198492 0.17768186601237085 0.734302196239392
chr21 48129895 7198558 0.14956521305521236 0.7827962779025751
chr22 51304566 4772400 0.09302096035662791 0.5001606064345048
chrMT 16571 69866 4.2161607627783475 3.499437161607893
chrX 155270560 30695439 0.19769001283952348 0.810800944400354
chrY 59373566 1459287 0.024578058862086874 0.773399853909015