BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1779369.sorted.bam
outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 12,465,586
number of mapped reads = 11,944,353 (95.82%)
number of supplementary alignments = 62,569 (0.5%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,012,449
number of mapped paired reads (second in pair) = 5,931,904
number of mapped paired reads (both in pair) = 11,838,722
number of mapped paired reads (singletons) = 105,631
number of mapped bases = 940,929,737 bp
number of sequenced bases = 940,694,432 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 913,890
duplication rate = 7.23%
>>>>>>> Insert size
mean insert size = 59,216.7699
std insert size = 2,358,989.7622
median insert size = 128
>>>>>>> Mapping quality
mean mapping quality = 49.1289
>>>>>>> ACTG content
number of A's = 278,137,519 bp (29.57%)
number of C's = 191,624,756 bp (20.37%)
number of T's = 276,030,590 bp (29.34%)
number of G's = 194,700,547 bp (20.7%)
number of N's = 201,020 bp (0.02%)
GC percentage = 41.07%
>>>>>>> Mismatches and indels
general error rate = 0.0035
number of mismatches = 3,087,619
number of insertions = 105,538
mapped reads with insertion percentage = 0.87%
number of deletions = 111,489
mapped reads with deletion percentage = 0.92%
homopolymer indels = 46.89%
>>>>>>> Coverage
mean coverageData = 0.3039X
std coverageData = 1.7422X
There is a 9.92% of reference with a coverageData >= 1X
There is a 5.92% of reference with a coverageData >= 2X
There is a 3.47% of reference with a coverageData >= 3X
There is a 2.33% of reference with a coverageData >= 4X
There is a 1.63% of reference with a coverageData >= 5X
There is a 1.19% of reference with a coverageData >= 6X
There is a 0.89% of reference with a coverageData >= 7X
There is a 0.69% of reference with a coverageData >= 8X
There is a 0.55% of reference with a coverageData >= 9X
There is a 0.45% of reference with a coverageData >= 10X
There is a 0.37% of reference with a coverageData >= 11X
There is a 0.31% of reference with a coverageData >= 12X
There is a 0.27% of reference with a coverageData >= 13X
There is a 0.23% of reference with a coverageData >= 14X
There is a 0.2% of reference with a coverageData >= 15X
There is a 0.18% of reference with a coverageData >= 16X
There is a 0.16% of reference with a coverageData >= 17X
There is a 0.14% of reference with a coverageData >= 18X
There is a 0.12% of reference with a coverageData >= 19X
There is a 0.11% of reference with a coverageData >= 20X
There is a 0.1% of reference with a coverageData >= 21X
There is a 0.09% 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 0.05% of reference with a coverageData >= 28X
There is a 0.05% of reference with a coverageData >= 29X
There is a 0.04% of reference with a coverageData >= 30X
There is a 0.04% of reference with a coverageData >= 31X
There is a 0.04% of reference with a coverageData >= 32X
There is a 0.03% of reference with a coverageData >= 33X
There is a 0.03% of reference with a coverageData >= 34X
There is a 0.03% of reference with a coverageData >= 35X
There is a 0.03% of reference with a coverageData >= 36X
There is a 0.02% of reference with a coverageData >= 37X
There is a 0.02% of reference with a coverageData >= 38X
There is a 0.02% of reference with a coverageData >= 39X
There is a 0.02% of reference with a coverageData >= 40X
There is a 0.02% of reference with a coverageData >= 41X
There is a 0.02% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 80255190 0.3219859179408022 2.455006523987903
chr2 243199373 71342844 0.2933512661646541 1.2289420262935566
chr3 198022430 59332621 0.29962575956673193 1.2232524336910968
chr4 191154276 23334783 0.12207303696413258 0.669276603516101
chr5 180915260 33881837 0.18728014983368457 0.8641218671689911
chr6 171115067 42424164 0.24792769417552224 2.20292867582128
chr7 159138663 122492905 0.7697243566762906 2.4314158132556374
chr8 146364022 27259290 0.1862431055631964 0.8901356315541458
chr9 141213431 127648603 0.9039409502060749 4.411109718180362
chr10 135534747 22230796 0.16402285385901816 1.715055265187479
chr11 135006516 18526026 0.13722319891582122 0.7748372803494844
chr12 133851895 47568872 0.355384374647815 1.3522924163640306
chr13 115169878 33251527 0.28871721996614425 1.244447467457055
chr14 107349540 40389506 0.3762429349953432 1.5744073142934745
chr15 102531392 26414499 0.2576235286067315 1.0455801866912169
chr16 90354753 33538573 0.3711877005518459 1.4271172744656222
chr17 81195210 20036036 0.24676376845382875 1.1541575385599046
chr18 78077248 23615620 0.30246481023511484 1.272219169216886
chr19 59128983 10401108 0.17590541004231378 1.3559036180928394
chr20 63025520 29553156 0.46890776942419515 1.6604486472124174
chr21 48129895 18937542 0.3934673449838193 1.4324693760988438
chr22 51304566 17659472 0.34420858369603985 1.5901200990965751
chrMT 16571 80 0.00482771106149297 0.06931381007706695
chrX 155270560 1820460 0.011724437652572387 0.1794505291461261
chrY 59373566 9014227 0.15182222674649523 0.787385619669476