BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714242.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 = 325,034
number of mapped reads = 46,957 (14.45%)
number of supplementary alignments = 1,031 (0.32%)
number of secondary alignments = 0
number of mapped bases = 5,008,133 bp
number of sequenced bases = 4,998,633 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 45,908
duplication rate = 29.47%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 11.1761
>>>>>>> ACTG content
number of A's = 109,874 bp (2.2%)
number of C's = 36,406 bp (0.73%)
number of T's = 49,435 bp (0.99%)
number of G's = 4,802,782 bp (96.08%)
number of N's = 136 bp (0%)
GC percentage = 96.81%
>>>>>>> Mismatches and indels
general error rate = 0.0342
number of mismatches = 127,018
number of insertions = 6,186
mapped reads with insertion percentage = 8.86%
number of deletions = 2,383
mapped reads with deletion percentage = 4.9%
homopolymer indels = 64.07%
>>>>>>> Coverage
mean coverageData = 0.0016X
std coverageData = 6.1048X
There is a 0% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% 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 17519 7.02866854642661E-5 0.11177030844640597
chr2 243199373 4829123 0.01985664247580112 21.77987502629107
chr3 198022430 4869 2.4588123678716596E-5 0.010234752328437912
chr4 191154276 5810 3.0394297849764032E-5 0.009697874303283659
chr5 180915260 3271 1.8080287975707523E-5 0.0054160732520857815
chr6 171115067 4117 2.405983337516386E-5 0.009626425187555361
chr7 159138663 10761 6.762027402479811E-5 0.06788009029887833
chr8 146364022 3742 2.5566392265443484E-5 0.015786500586220952
chr9 141213431 4375 3.098147229352426E-5 0.013184658747153041
chr10 135534747 15369 1.133952756779042E-4 0.1420207981851276
chr11 135006516 3923 2.9057856733374263E-5 0.023065995427153384
chr12 133851895 10859 8.112697993554742E-5 0.053510860076140435
chr13 115169878 2172 1.8859097862376826E-5 0.005831088452209553
chr14 107349540 5973 5.564066692786946E-5 0.04890194116089072
chr15 102531392 3737 3.6447374088123175E-5 0.010686340874853267
chr16 90354753 2623 2.9030016827117E-5 0.013406120576334123
chr17 81195210 6534 8.047272739364797E-5 0.07909194032647039
chr18 78077248 1348 1.7264952781122614E-5 0.004532489346488404
chr19 59128983 2473 4.1823820984710664E-5 0.011472827210205901
chr20 63025520 2027 3.2161575184147625E-5 0.016676110602305668
chr21 48129895 1086 2.256393869132688E-5 0.006720782875991877
chr22 51304566 870 1.6957555005922866E-5 0.004566788363211042
chrMT 16571 7756 0.46804658741174343 2.317519494655438
chrX 155270560 56067 3.610922766041418E-4 0.051379936491310535
chrY 59373566 1729 2.9120703310965018E-5 0.012328942497769313