BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6004078.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 = 1,839,821
number of mapped reads = 1,678,700 (91.24%)
number of supplementary alignments = 14,142 (0.77%)
number of secondary alignments = 0
number of mapped bases = 112,648,142 bp
number of sequenced bases = 112,597,337 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 77,139
duplication rate = 3.79%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.3229
>>>>>>> ACTG content
number of A's = 31,700,384 bp (28.15%)
number of C's = 20,932,629 bp (18.59%)
number of T's = 35,575,232 bp (31.6%)
number of G's = 24,367,886 bp (21.64%)
number of N's = 21,206 bp (0.02%)
GC percentage = 40.23%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 944,919
number of insertions = 7,856
mapped reads with insertion percentage = 0.46%
number of deletions = 29,355
mapped reads with deletion percentage = 1.73%
homopolymer indels = 46.03%
>>>>>>> Coverage
mean coverageData = 0.0364X
std coverageData = 0.3189X
There is a 3% of reference with a coverageData >= 1X
There is a 0.48% of reference with a coverageData >= 2X
There is a 0.09% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% 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 8712116 0.03495323688682003 0.5284323527074021
chr2 243199373 10357945 0.042590344178231085 0.3348188472782836
chr3 198022430 5713713 0.02885386771589461 0.1974197759168142
chr4 191154276 9634905 0.05040381623479875 0.2736587099479993
chr5 180915260 6448089 0.03564148762243716 0.2208246112882949
chr6 171115067 6713649 0.0392347039784638 0.23896629084571072
chr7 159138663 6114573 0.03842292554638341 0.5139594564596974
chr8 146364022 8223411 0.05618464761784149 0.4863906593110767
chr9 141213431 3681279 0.026068901335596046 0.24076114952540786
chr10 135534747 4851575 0.035795802238078475 0.2844117973306307
chr11 135006516 4709846 0.034886064314110586 0.2618052007960417
chr12 133851895 5335911 0.03986429179803543 0.2356103132385816
chr13 115169878 3334107 0.028949470624602035 0.202393742862418
chr14 107349540 2007330 0.018699008863941102 0.17064881448631636
chr15 102531392 4213848 0.041098125342919366 0.23864943372432307
chr16 90354753 3353503 0.03711484884475308 0.2376493177907606
chr17 81195210 1293371 0.01592915394885979 0.16096122241325614
chr18 78077248 2881638 0.036907525224249706 0.4242571895449391
chr19 59128983 1689656 0.028575766303979896 0.37779163738365584
chr20 63025520 2107175 0.033433678928789484 0.2187344011547996
chr21 48129895 1906608 0.03961379928213016 0.24387903002243966
chr22 51304566 882732 0.017205720052285406 0.1501755367539556
chrMT 16571 43812 2.6438959628266248 2.5570448762578604
chrX 155270560 8138219 0.05241314902193951 0.290695364258998
chrY 59373566 299131 0.005038117467965458 0.10799284312586087