BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524991.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,011,048
number of mapped reads = 942,209 (93.19%)
number of supplementary alignments = 2,337 (0.23%)
number of secondary alignments = 0
number of mapped bases = 55,444,230 bp
number of sequenced bases = 55,427,387 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 26,125
duplication rate = 2.14%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.1597
>>>>>>> ACTG content
number of A's = 14,042,107 bp (25.33%)
number of C's = 10,311,281 bp (18.6%)
number of T's = 17,722,459 bp (31.97%)
number of G's = 13,350,909 bp (24.09%)
number of N's = 631 bp (0%)
GC percentage = 42.69%
>>>>>>> Mismatches and indels
general error rate = 0.0048
number of mismatches = 259,379
number of insertions = 3,454
mapped reads with insertion percentage = 0.37%
number of deletions = 9,745
mapped reads with deletion percentage = 1.03%
homopolymer indels = 43.41%
>>>>>>> Coverage
mean coverageData = 0.0179X
std coverageData = 0.1767X
There is a 1.65% of reference with a coverageData >= 1X
There is a 0.1% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% 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 4474338 0.01795116089199232 0.2703325464805947
chr2 243199373 4553146 0.018721865701520537 0.18982552364181995
chr3 198022430 3637993 0.018371620831034143 0.14367004082081383
chr4 191154276 3437058 0.01798054467795426 0.15493029936498331
chr5 180915260 3325879 0.01838362888791139 0.14480598722819807
chr6 171115067 3399447 0.01986643876310436 0.17087615216281665
chr7 159138663 3096216 0.019456089058634357 0.20114223009974325
chr8 146364022 2641047 0.018044372953894366 0.19055624089617856
chr9 141213431 2390189 0.016926074121094047 0.16151800204794522
chr10 135534747 2694888 0.01988337352339618 0.18698525541576164
chr11 135006516 2586329 0.019157067944779792 0.17885388623209758
chr12 133851895 2680844 0.02002843515962176 0.15189592255316559
chr13 115169878 1804192 0.01566548503246656 0.13307755637647753
chr14 107349540 1579110 0.014709983852748694 0.13204192477543858
chr15 102531392 1647274 0.016066045411731074 0.1371498235099332
chr16 90354753 1691341 0.01871889351520888 0.15131824501278787
chr17 81195210 1564142 0.01926396889668738 0.15764780414894655
chr18 78077248 1527871 0.019568709696325362 0.2555420695029295
chr19 59128983 1016066 0.017183891020077245 0.1980077323922675
chr20 63025520 1235775 0.019607533583221527 0.15160450133222825
chr21 48129895 720698 0.014974019785416112 0.13875932954102527
chr22 51304566 682607 0.013304995114859757 0.12217009582374976
chrMT 16571 1018 0.061432623257498035 0.2862130397819123
chrX 155270560 2891746 0.018623916858417976 0.15375071603439341
chrY 59373566 165016 0.00277928396620139 0.08527111829988894