BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231883.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,461,523
number of mapped reads = 1,165,293 (79.73%)
number of supplementary alignments = 7,199 (0.49%)
number of secondary alignments = 0
number of mapped bases = 73,840,564 bp
number of sequenced bases = 73,796,445 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 150,896
duplication rate = 10.78%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8156
>>>>>>> ACTG content
number of A's = 19,261,302 bp (26.1%)
number of C's = 12,766,774 bp (17.3%)
number of T's = 24,622,977 bp (33.37%)
number of G's = 17,142,153 bp (23.23%)
number of N's = 3,239 bp (0%)
GC percentage = 40.53%
>>>>>>> Mismatches and indels
general error rate = 0.0082
number of mismatches = 594,494
number of insertions = 6,087
mapped reads with insertion percentage = 0.52%
number of deletions = 24,607
mapped reads with deletion percentage = 2.09%
homopolymer indels = 49.63%
>>>>>>> Coverage
mean coverageData = 0.0239X
std coverageData = 0.2539X
There is a 1.51% of reference with a coverageData >= 1X
There is a 0.53% of reference with a coverageData >= 2X
There is a 0.2% of reference with a coverageData >= 3X
There is a 0.08% of reference with a coverageData >= 4X
There is a 0.03% 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% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% 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 6509234 0.026115216780141944 0.26509245381806973
chr2 243199373 6418204 0.026390709485916316 0.34045551112453626
chr3 198022430 5091917 0.025713839588777897 0.23534255155375194
chr4 191154276 4520935 0.023650713416423916 0.2365001293573493
chr5 180915260 4311156 0.023829697948089066 0.22724415627063468
chr6 171115067 4610952 0.026946499106358646 0.2581627644781988
chr7 159138663 4221799 0.02652905912625394 0.284014116099856
chr8 146364022 3984679 0.027224443176342886 0.3417999027145677
chr9 141213431 3031732 0.021469147647860776 0.22903973678425657
chr10 135534747 3440902 0.025387600421019712 0.24733657545873772
chr11 135006516 3498864 0.025916260219617845 0.2816588171638717
chr12 133851895 3305636 0.0246962211480084 0.23189998324373032
chr13 115169878 2352874 0.02042959531484439 0.2110336544693589
chr14 107349540 2352424 0.021913684958500986 0.21856643614093077
chr15 102531392 2273507 0.022173765084550885 0.22534741018487445
chr16 90354753 2086061 0.023087451747004387 0.22131416795746628
chr17 81195210 2027871 0.024975254082106567 0.24115516866225203
chr18 78077248 2040210 0.026130659728170746 0.2824601073519338
chr19 59128983 1469859 0.02485851989032181 0.23974846507589093
chr20 63025520 1647153 0.026134699086973023 0.2387267805440519
chr21 48129895 970041 0.020154646088465393 0.20874240531900623
chr22 51304566 810083 0.015789686243520704 0.1778980139373581
chrMT 16571 28950 1.7470279403777684 2.3943366398285875
chrX 155270560 2380368 0.015330452855969606 0.18217057262913694
chrY 59373566 455153 0.007665919880911314 0.12874617852420508