BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6240224.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 = 2,469,719
number of mapped reads = 1,947,379 (78.85%)
number of supplementary alignments = 20,710 (0.84%)
number of secondary alignments = 0
number of mapped bases = 128,927,795 bp
number of sequenced bases = 128,874,664 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 217,797
duplication rate = 8.58%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.8863
>>>>>>> ACTG content
number of A's = 37,125,483 bp (28.81%)
number of C's = 24,158,872 bp (18.75%)
number of T's = 40,549,103 bp (31.46%)
number of G's = 27,029,858 bp (20.97%)
number of N's = 11,348 bp (0.01%)
GC percentage = 39.72%
>>>>>>> Mismatches and indels
general error rate = 0.008
number of mismatches = 1,014,986
number of insertions = 9,378
mapped reads with insertion percentage = 0.48%
number of deletions = 30,227
mapped reads with deletion percentage = 1.54%
homopolymer indels = 47.41%
>>>>>>> Coverage
mean coverageData = 0.0416X
std coverageData = 0.4675X
There is a 2.14% of reference with a coverageData >= 1X
There is a 0.98% of reference with a coverageData >= 2X
There is a 0.48% of reference with a coverageData >= 3X
There is a 0.24% of reference with a coverageData >= 4X
There is a 0.12% of reference with a coverageData >= 5X
There is a 0.06% 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% 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 9650064 0.03871630875495392 0.7218705025227514
chr2 243199373 10554450 0.04339834379424983 0.4829546052555227
chr3 198022430 9457091 0.047757675734006494 0.3725761375462815
chr4 191154276 8257806 0.04319969279682763 0.3691628784661478
chr5 180915260 6996431 0.03867242044700928 0.3362397836280654
chr6 171115067 9381664 0.05482663896569669 0.42662428915211015
chr7 159138663 6889489 0.043292364470851434 0.5016177811123383
chr8 146364022 6650185 0.045435926870061004 0.7377351662606578
chr9 141213431 5158553 0.036530186707240335 0.4456518679803468
chr10 135534747 6953170 0.05130175216249159 0.4738569228260009
chr11 135006516 5721284 0.042377836044595066 0.43227215335018476
chr12 133851895 6131431 0.04580757709855359 0.3698593447620791
chr13 115169878 4319100 0.03750199335975679 0.3357288539947208
chr14 107349540 3754311 0.03497277212366257 0.3324310474380351
chr15 102531392 3402648 0.033186402072840286 0.31303777055337056
chr16 90354753 3473161 0.03843916213240049 0.3602132341770618
chr17 81195210 3234340 0.039834123219830334 0.37961508172899083
chr18 78077248 3462284 0.04434433959557591 0.757766260016079
chr19 59128983 2209463 0.03736683582059918 0.5019023600672522
chr20 63025520 2179490 0.03458107128667879 0.31965800300028446
chr21 48129895 1430657 0.029724914213920477 0.3014218020592251
chr22 51304566 1277812 0.02490639916922794 0.2594209795118461
chrMT 16571 27002 1.6294731760304146 2.142692388131467
chrX 155270560 8018099 0.05163953166653099 0.43424658030805663
chrY 59373566 337810 0.005689568991022032 0.13790473779542928