BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068171.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 = 2,122,838
number of mapped reads = 1,912,020 (90.07%)
number of supplementary alignments = 19,681 (0.93%)
number of secondary alignments = 0
number of mapped bases = 129,767,172 bp
number of sequenced bases = 129,695,289 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 116,433
duplication rate = 4.97%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 40.0903
>>>>>>> ACTG content
number of A's = 36,904,994 bp (28.46%)
number of C's = 23,480,735 bp (18.1%)
number of T's = 41,860,058 bp (32.28%)
number of G's = 27,309,716 bp (21.06%)
number of N's = 139,786 bp (0.11%)
GC percentage = 39.16%
>>>>>>> Mismatches and indels
general error rate = 0.0092
number of mismatches = 1,174,169
number of insertions = 9,467
mapped reads with insertion percentage = 0.49%
number of deletions = 43,586
mapped reads with deletion percentage = 2.25%
homopolymer indels = 45.56%
>>>>>>> Coverage
mean coverageData = 0.0419X
std coverageData = 0.4826X
There is a 3.05% of reference with a coverageData >= 1X
There is a 0.77% of reference with a coverageData >= 2X
There is a 0.21% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% 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 15870709 0.06367369893132584 1.271015485371541
chr2 243199373 29915612 0.12300859015783729 0.5556484626803416
chr3 198022430 8993668 0.04541742064270194 0.28076842699467286
chr4 191154276 2674469 0.013991154453693727 0.15081819425230863
chr5 180915260 5663527 0.031304860629224975 0.22915060427545184
chr6 171115067 2951711 0.017249860294301263 0.17853197584135622
chr7 159138663 3379346 0.021235229304396003 0.2020833616993917
chr8 146364022 15622772 0.10673915479037602 0.5146029741836402
chr9 141213431 1443116 0.010219396198935212 0.18462282465102783
chr10 135534747 4490913 0.03313477244326136 0.3599080835913699
chr11 135006516 14273225 0.10572248972042209 0.5793819628478982
chr12 133851895 1410860 0.010540455927052807 0.1297299677522553
chr13 115169878 3294813 0.02860828766355036 0.21775801027142533
chr14 107349540 465152 0.004333060020564597 0.08855523751729867
chr15 102531392 1218291 0.011882126792933817 0.13687110727692514
chr16 90354753 1206643 0.013354504992117017 0.18710999865094835
chr17 81195210 3203434 0.03945348500237884 0.290632352796076
chr18 78077248 1404706 0.0179912335024923 0.2737574825480471
chr19 59128983 1682621 0.02845678911812165 0.8514556649592391
chr20 63025520 1837952 0.02916202833391934 0.22361346790531472
chr21 48129895 414577 0.008613710875537958 0.1408468697441381
chr22 51304566 2172918 0.04235330633144816 0.2581753447690533
chrMT 16571 5791 0.34946593446382235 0.7168431813254259
chrX 155270560 5936738 0.038234794799477764 0.3012107454939349
chrY 59373566 233608 0.0039345455518033055 0.09459982413008938