BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094023.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 499,408
number of mapped reads = 458,442 (91.8%)
number of supplementary alignments = 27,594 (5.53%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 230,433
number of mapped paired reads (second in pair) = 228,009
number of mapped paired reads (both in pair) = 451,978
number of mapped paired reads (singletons) = 6,464
number of mapped bases = 60,013,120 bp
number of sequenced bases = 59,127,044 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 443,800
duplication rate = 45.05%
>>>>>>> Insert size
mean insert size = 328,097.1978
std insert size = 5,385,387.6823
median insert size = 179
>>>>>>> Mapping quality
mean mapping quality = 44.1296
>>>>>>> ACTG content
number of A's = 17,029,932 bp (28.8%)
number of C's = 12,643,479 bp (21.38%)
number of T's = 16,060,439 bp (27.16%)
number of G's = 13,392,644 bp (22.65%)
number of N's = 550 bp (0%)
GC percentage = 44.03%
>>>>>>> Mismatches and indels
general error rate = 0.0319
number of mismatches = 1,794,214
number of insertions = 32,467
mapped reads with insertion percentage = 6.84%
number of deletions = 130,322
mapped reads with deletion percentage = 27.32%
homopolymer indels = 34.98%
>>>>>>> Coverage
mean coverageData = 0.0194X
std coverageData = 9.1925X
There is a 0.03% of reference with a coverageData >= 1X
There is a 0.02% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% 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 1080639 0.004335551886147557 1.13416668886779
chr2 243199373 2519836 0.010361194475612403 2.8469788248105
chr3 198022430 1360744 0.006871666002684645 3.506132332699899
chr4 191154276 1322706 0.006919573172404472 2.5353485850832516
chr5 180915260 589610 0.003259039618880132 1.2779950867680772
chr6 171115067 1559670 0.009114743823230948 4.239552370028107
chr7 159138663 1749616 0.010994286159108928 2.012535121875583
chr8 146364022 1176789 0.00804015210787252 4.330804328405086
chr9 141213431 749066 0.005304495434290525 1.2850446974201604
chr10 135534747 958559 0.007072422542685678 1.952136375570725
chr11 135006516 855728 0.006338419991521002 1.3559952397242363
chr12 133851895 3421122 0.02555901057657794 9.575949278127537
chr13 115169878 1377565 0.011961157065739011 4.971368933224104
chr14 107349540 248431 0.002314225100545377 0.33790653846403124
chr15 102531392 412976 0.004027800578382862 0.9751900414562438
chr16 90354753 691461 0.00765273521360852 1.817495448392138
chr17 81195210 669816 0.008249452153643054 1.6162168996595263
chr18 78077248 243127 0.0031139289130682475 0.812510666870143
chr19 59128983 518287 0.008765363003114732 1.3682456230757194
chr20 63025520 495653 0.007864322261839331 2.345176740676449
chr21 48129895 101094 0.002100440900608655 0.39209710835073297
chr22 51304566 393043 0.0076609750484976325 1.0590892661080746
chrMT 16571 12951299 781.5641180375354 3415.626900514808
chrX 155270560 24148432 0.15552485931653753 13.40605653243031
chrY 59373566 417851 0.0070376604969288855 1.929344970860949