BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549013.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,306,390
number of mapped reads = 4,631,988 (87.29%)
number of secondary alignments = 0
number of mapped bases = 182,887,298 bp
number of sequenced bases = 182,866,264 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 150,074
duplication rate = 2.01%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 38.3179
>>>>>>> ACTG content
number of A's = 52,918,993 bp (28.94%)
number of C's = 38,516,060 bp (21.06%)
number of T's = 53,277,548 bp (29.13%)
number of G's = 38,147,429 bp (20.86%)
number of N's = 6,234 bp (0%)
GC percentage = 41.92%
>>>>>>> Mismatches and indels
general error rate = 0.0032
number of mismatches = 577,633
number of insertions = 6,776
mapped reads with insertion percentage = 0.15%
number of deletions = 16,158
mapped reads with deletion percentage = 0.35%
homopolymer indels = 39.5%
>>>>>>> Coverage
mean coverageData = 0.0591X
std coverageData = 0.7279X
There is a 5.12% of reference with a coverageData >= 1X
There is a 0.57% of reference with a coverageData >= 2X
There is a 0.08% 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 0.01% 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 14431217 0.05789841943864204 0.8564266758045821
chr2 243199373 15078428 0.06200027497603787 0.4509154275944181
chr3 198022430 12372261 0.06247908885877221 0.2817058032381496
chr4 191154276 12025683 0.06291087623904369 0.2900607181653364
chr5 180915260 11405550 0.06304360395026931 0.28948250602443226
chr6 171115067 10757970 0.06286979977046674 0.30879888378495607
chr7 159138663 10233613 0.06430626478243065 0.6241986881919651
chr8 146364022 9398377 0.06421234447902778 2.6400901621310164
chr9 141213431 7733377 0.05476374977391492 0.4406922705335421
chr10 135534747 8427873 0.06218237895851165 0.4117127527797987
chr11 135006516 8360785 0.06192875164632795 0.45351740729985257
chr12 133851895 8286387 0.061907132506416884 0.2949283893142269
chr13 115169878 5814818 0.050489052354470675 0.2472154253186726
chr14 107349540 5591170 0.05208378163520775 0.32403531726649343
chr15 102531392 5231528 0.051023670877305555 0.25257575342581645
chr16 90354753 5011767 0.05546766311231021 0.30170817695948043
chr17 81195210 4847539 0.059702278003837914 0.29971084390802083
chr18 78077248 4815694 0.06167858272873552 0.8189179470723402
chr19 59128983 3860149 0.06528353447242616 0.8574238101889146
chr20 63025520 3560789 0.0564975743159279 0.2815760777773617
chr21 48129895 2314862 0.04809613650725812 0.28487435861422045
chr22 51304566 2025285 0.03947572619559826 0.27308827536049207
chrMT 16571 9358 0.5647215014181401 0.9337261692558919
chrX 155270560 10655084 0.06862269318794238 0.37636359124104807
chrY 59373566 637734 0.010741042571032368 0.1559793065405934