BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6240074.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 = 1,886,261
number of mapped reads = 494,484 (26.22%)
number of supplementary alignments = 4,138 (0.22%)
number of secondary alignments = 0
number of mapped bases = 31,933,414 bp
number of sequenced bases = 31,917,852 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 75,994
duplication rate = 11.13%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7634
>>>>>>> ACTG content
number of A's = 8,890,933 bp (27.86%)
number of C's = 5,599,519 bp (17.54%)
number of T's = 10,583,796 bp (33.16%)
number of G's = 6,840,773 bp (21.43%)
number of N's = 2,831 bp (0.01%)
GC percentage = 38.98%
>>>>>>> Mismatches and indels
general error rate = 0.0093
number of mismatches = 291,031
number of insertions = 2,489
mapped reads with insertion percentage = 0.5%
number of deletions = 9,015
mapped reads with deletion percentage = 1.8%
homopolymer indels = 47.35%
>>>>>>> Coverage
mean coverageData = 0.0103X
std coverageData = 0.2164X
There is a 0.54% of reference with a coverageData >= 1X
There is a 0.23% of reference with a coverageData >= 2X
There is a 0.12% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.02% 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% 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 2370442 0.009510275202082646 0.25291087512873917
chr2 243199373 3444482 0.01416320263292784 0.29185456543804883
chr3 198022430 2494542 0.012597269915332318 0.19993930706487087
chr4 191154276 2116957 0.011074599241504805 0.1811952488802197
chr5 180915260 1651106 0.009126405367905394 0.16261587134239627
chr6 171115067 1268064 0.0074105923121311115 0.15897929506620637
chr7 159138663 1977179 0.012424252929660469 0.21810944135257265
chr8 146364022 1523022 0.01040571295587928 0.39533633891493064
chr9 141213431 1643579 0.011638970800164185 0.2100750389326778
chr10 135534747 1296171 0.009563385247622147 0.17385816364370288
chr11 135006516 1712782 0.012686661731201181 0.206420150503827
chr12 133851895 1630258 0.012179566079359579 0.20333665717457328
chr13 115169878 910802 0.007908335198549051 0.15369162898911756
chr14 107349540 867435 0.00808047244543386 0.15543058102331445
chr15 102531392 1006708 0.009818534405540891 0.17319613762644576
chr16 90354753 795081 0.00879954815437324 0.17023306814612682
chr17 81195210 640621 0.007889886607843 0.15524520893546215
chr18 78077248 1257494 0.016105767457377598 0.3157559627887314
chr19 59128983 505824 0.008554586504557333 0.18539538230677882
chr20 63025520 562717 0.00892839916275185 0.16644869582761507
chr21 48129895 513204 0.01066289465206604 0.22875188338934743
chr22 51304566 268553 0.0052344853672478195 0.11490944477363203
chrMT 16571 13655 0.8240299318085813 1.6517574539310433
chrX 155270560 1380400 0.008890288023692322 0.17757841640276228
chrY 59373566 82336 0.0013867450710304313 0.06482507775673144