BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472440.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,254,074
number of mapped reads = 19,103,987 (99.22%)
number of supplementary alignments = 77,168 (0.4%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 9,580,002
number of mapped paired reads (second in pair) = 9,523,985
number of mapped paired reads (both in pair) = 19,014,808
number of mapped paired reads (singletons) = 89,179
number of mapped bases = 1,875,232,891 bp
number of sequenced bases = 1,875,015,091 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 12,336,736
duplication rate = 47.64%
>>>>>>> Insert size
mean insert size = 18,573.1138
std insert size = 1,343,603.7861
median insert size = 213
>>>>>>> Mapping quality
mean mapping quality = 54.7203
>>>>>>> ACTG content
number of A's = 512,821,068 bp (27.35%)
number of C's = 425,823,524 bp (22.71%)
number of T's = 513,663,285 bp (27.4%)
number of G's = 422,470,796 bp (22.53%)
number of N's = 236,418 bp (0.01%)
GC percentage = 45.24%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 9,892,220
number of insertions = 117,673
mapped reads with insertion percentage = 0.61%
number of deletions = 89,581
mapped reads with deletion percentage = 0.46%
homopolymer indels = 45.43%
>>>>>>> Coverage
mean coverageData = 0.6058X
std coverageData = 19.3737X
There is a 5.08% of reference with a coverageData >= 1X
There is a 2.21% of reference with a coverageData >= 2X
There is a 0.92% of reference with a coverageData >= 3X
There is a 0.68% of reference with a coverageData >= 4X
There is a 0.51% of reference with a coverageData >= 5X
There is a 0.46% of reference with a coverageData >= 6X
There is a 0.42% of reference with a coverageData >= 7X
There is a 0.4% of reference with a coverageData >= 8X
There is a 0.38% of reference with a coverageData >= 9X
There is a 0.36% of reference with a coverageData >= 10X
There is a 0.35% of reference with a coverageData >= 11X
There is a 0.34% of reference with a coverageData >= 12X
There is a 0.33% of reference with a coverageData >= 13X
There is a 0.32% of reference with a coverageData >= 14X
There is a 0.31% of reference with a coverageData >= 15X
There is a 0.31% of reference with a coverageData >= 16X
There is a 0.3% of reference with a coverageData >= 17X
There is a 0.29% of reference with a coverageData >= 18X
There is a 0.29% of reference with a coverageData >= 19X
There is a 0.28% of reference with a coverageData >= 20X
There is a 0.28% of reference with a coverageData >= 21X
There is a 0.27% of reference with a coverageData >= 22X
There is a 0.26% of reference with a coverageData >= 23X
There is a 0.26% of reference with a coverageData >= 24X
There is a 0.26% of reference with a coverageData >= 25X
There is a 0.25% of reference with a coverageData >= 26X
There is a 0.25% of reference with a coverageData >= 27X
There is a 0.24% of reference with a coverageData >= 28X
There is a 0.24% of reference with a coverageData >= 29X
There is a 0.24% of reference with a coverageData >= 30X
There is a 0.23% of reference with a coverageData >= 31X
There is a 0.23% of reference with a coverageData >= 32X
There is a 0.23% of reference with a coverageData >= 33X
There is a 0.22% of reference with a coverageData >= 34X
There is a 0.22% of reference with a coverageData >= 35X
There is a 0.22% of reference with a coverageData >= 36X
There is a 0.21% of reference with a coverageData >= 37X
There is a 0.21% of reference with a coverageData >= 38X
There is a 0.21% of reference with a coverageData >= 39X
There is a 0.21% of reference with a coverageData >= 40X
There is a 0.2% of reference with a coverageData >= 41X
There is a 0.2% of reference with a coverageData >= 42X
There is a 0.2% of reference with a coverageData >= 43X
There is a 0.2% of reference with a coverageData >= 44X
There is a 0.19% of reference with a coverageData >= 45X
There is a 0.19% of reference with a coverageData >= 46X
There is a 0.19% of reference with a coverageData >= 47X
There is a 0.19% of reference with a coverageData >= 48X
There is a 0.18% of reference with a coverageData >= 49X
There is a 0.18% of reference with a coverageData >= 50X
There is a 0.18% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 178404325 0.7157628104766086 20.656237628193306
chr2 243199373 180231979 0.741087350582931 23.75160901701015
chr3 198022430 148333826 0.7490758799394593 18.25076912558515
chr4 191154276 57633797 0.30150409504833675 14.722143515861422
chr5 180915260 64528552 0.35667832553207507 12.072411499361257
chr6 171115067 139259081 0.8138329572111846 18.08802119282275
chr7 159138663 137384241 0.8632989520591863 30.036794076070176
chr8 146364022 138871635 0.9488099131356201 23.17981507845586
chr9 141213431 72320052 0.5121329570981106 15.389045949060291
chr10 135534747 20302370 0.14979457629415135 5.886126930584001
chr11 135006516 51055364 0.3781696284940795 13.48301892939276
chr12 133851895 94277364 0.7043408985730086 17.456085195956128
chr13 115169878 59083286 0.5130098861440141 15.739035160836542
chr14 107349540 46954599 0.437399163517608 19.21701802870763
chr15 102531392 23237117 0.22663417073280348 7.4524565082502106
chr16 90354753 115832195 1.2819712428409826 31.801097399085307
chr17 81195210 78068685 0.9614937260461547 24.960147843771775
chr18 78077248 17958022 0.2300032654839474 8.300763657574818
chr19 59128983 32396301 0.5478920718118896 15.805293581473382
chr20 63025520 83534065 1.325400647229884 39.76500589298324
chr21 48129895 14283450 0.2967687754149474 18.47662643695444
chr22 51304566 11182700 0.21796695444222255 5.94023198369512
chrMT 16571 2860 0.17259067044837367 0.5380007940657742
chrX 155270560 109706605 0.7065512290288642 17.727770234137115
chrY 59373566 390420 0.006575653549257931 0.500214048123243