BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818831.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,472,351
number of mapped reads = 2,438,543 (98.63%)
number of supplementary alignments = 35,916 (1.45%)
number of secondary alignments = 0
number of mapped bases = 226,055,958 bp
number of sequenced bases = 225,917,541 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 644,306
duplication rate = 22.68%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.3386
>>>>>>> ACTG content
number of A's = 65,281,674 bp (28.9%)
number of C's = 46,262,420 bp (20.48%)
number of T's = 63,902,917 bp (28.29%)
number of G's = 50,466,947 bp (22.34%)
number of N's = 3,583 bp (0%)
GC percentage = 42.82%
>>>>>>> Mismatches and indels
general error rate = 0.0062
number of mismatches = 1,325,786
number of insertions = 30,547
mapped reads with insertion percentage = 1.21%
number of deletions = 70,940
mapped reads with deletion percentage = 2.84%
homopolymer indels = 40.18%
>>>>>>> Coverage
mean coverageData = 0.073X
std coverageData = 0.8333X
There is a 4.65% of reference with a coverageData >= 1X
There is a 1.48% of reference with a coverageData >= 2X
There is a 0.54% of reference with a coverageData >= 3X
There is a 0.22% of reference with a coverageData >= 4X
There is a 0.1% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% 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 21348489 0.08565069532966178 1.259965759923883
chr2 243199373 17001274 0.06990673450461568 1.1495321440636728
chr3 198022430 14275916 0.0720924190254609 0.3843243331371561
chr4 191154276 11334579 0.05929545096861971 0.4726971599061102
chr5 180915260 9961922 0.055064022791665 0.3611112990972078
chr6 171115067 11128403 0.06503461790421997 0.41119774729333214
chr7 159138663 20153295 0.12663984113024754 1.8421877614573923
chr8 146364022 19714937 0.13469797242931736 0.7255372319573713
chr9 141213431 8337085 0.05903889552828725 0.703073291642771
chr10 135534747 10489850 0.0773960200774197 1.1284881790125705
chr11 135006516 9978858 0.0739138990891373 0.4981301806575702
chr12 133851895 8975635 0.06705646565556656 0.37335524260544345
chr13 115169878 6979448 0.06060133188645038 0.3504478481192835
chr14 107349540 6631399 0.06177389302273675 0.4014366407525947
chr15 102531392 6259989 0.061054364696423905 0.3537038194006778
chr16 90354753 5643605 0.06246052158429341 0.8555663041188295
chr17 81195210 5666575 0.06978952329823397 0.5235830994880879
chr18 78077248 4392158 0.056254006288746244 0.8201814694305858
chr19 59128983 3861657 0.06530903803977146 1.1178086514353625
chr20 63025520 9426114 0.14956027336228245 0.6075506691259501
chr21 48129895 2164540 0.04497288016107245 0.3861830890621821
chr22 51304566 2082176 0.04058461385288787 0.32662385987221276
chrMT 16571 135938 8.203367328465392 5.777120537097879
chrX 155270560 9280733 0.05977136296797023 0.4290389161796057
chrY 59373566 831383 0.014002578184372486 1.0799150329955574