BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714109.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 620,550
number of mapped reads = 420,814 (67.81%)
number of supplementary alignments = 14,686 (2.37%)
number of secondary alignments = 0
number of mapped bases = 54,198,946 bp
number of sequenced bases = 52,983,846 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 369,796
duplication rate = 43.21%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 50.837
>>>>>>> ACTG content
number of A's = 14,355,003 bp (27.09%)
number of C's = 10,616,496 bp (20.04%)
number of T's = 13,527,662 bp (25.53%)
number of G's = 14,484,339 bp (27.34%)
number of N's = 346 bp (0%)
GC percentage = 47.37%
>>>>>>> Mismatches and indels
general error rate = 0.0455
number of mismatches = 2,265,924
number of insertions = 56,484
mapped reads with insertion percentage = 12.77%
number of deletions = 203,653
mapped reads with deletion percentage = 44.84%
homopolymer indels = 29.92%
>>>>>>> Coverage
mean coverageData = 0.0175X
std coverageData = 5.2357X
There is a 0.05% of reference with a coverageData >= 1X
There is a 0.03% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.02% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 4147298 0.016639067872171922 2.7436981876294904
chr2 243199373 7446409 0.030618536997626223 15.544597792328812
chr3 198022430 2885765 0.01457291984549427 2.9150954237291624
chr4 191154276 1865607 0.00975969274158429 1.6866284630101656
chr5 180915260 3338793 0.018455010373364857 3.882439007175342
chr6 171115067 2167553 0.012667224681038754 2.3466068235987256
chr7 159138663 2228614 0.014004227244261817 2.781772509685599
chr8 146364022 3070029 0.020975298150798287 5.2657780480194285
chr9 141213431 1493559 0.010576607263370012 1.716020762572134
chr10 135534747 2113765 0.015595742396597383 3.0245632881702456
chr11 135006516 2338817 0.017323734211465762 2.562226146766841
chr12 133851895 2473412 0.018478722322160624 2.9013827600145965
chr13 115169878 1555762 0.013508410593262936 2.035446450887984
chr14 107349540 2477632 0.02308004300717078 5.489580666605478
chr15 102531392 1960314 0.019119159135184666 2.9003385511921085
chr16 90354753 974184 0.010781768171066772 1.4685642360429438
chr17 81195210 1385937 0.017069196569600598 2.657834394755412
chr18 78077248 948751 0.012151440071248413 1.5385073736123196
chr19 59128983 1193852 0.020190639842393367 2.641161201673715
chr20 63025520 1162980 0.018452525262782443 2.2462710368600773
chr21 48129895 528877 0.010988534257138936 2.261758350445549
chr22 51304566 967178 0.018851694408641914 4.136699047475432
chrMT 16571 308842 18.637499245670146 134.940128276436
chrX 155270560 4695009 0.03023759945220781 2.873048995928368
chrY 59373566 470007 0.007916098554700251 2.5723672481808917