BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714081.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 = 577,850
number of mapped reads = 187,488 (32.45%)
number of supplementary alignments = 4,619 (0.8%)
number of secondary alignments = 0
number of mapped bases = 23,633,193 bp
number of sequenced bases = 23,194,545 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 180,553
duplication rate = 45.08%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 34.0668
>>>>>>> ACTG content
number of A's = 5,328,016 bp (22.97%)
number of C's = 4,022,792 bp (17.34%)
number of T's = 5,443,919 bp (23.47%)
number of G's = 8,399,414 bp (36.21%)
number of N's = 404 bp (0%)
GC percentage = 53.56%
>>>>>>> Mismatches and indels
general error rate = 0.0415
number of mismatches = 902,675
number of insertions = 18,994
mapped reads with insertion percentage = 9.18%
number of deletions = 59,086
mapped reads with deletion percentage = 30.07%
homopolymer indels = 59%
>>>>>>> Coverage
mean coverageData = 0.0076X
std coverageData = 12.5751X
There is a 0.01% of reference with a coverageData >= 1X
There is a 0.01% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0.01% 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 547303 0.002195793927430175 1.1189122308061554
chr2 243199373 4290603 0.017642327556494152 18.45739188796828
chr3 198022430 955326 0.004824332273874227 2.0968297592473966
chr4 191154276 64552 3.376958201029204E-4 0.10075673076960501
chr5 180915260 326423 0.0018042867141224018 0.8787377243685115
chr6 171115067 80813 4.7227284783753144E-4 0.06829597658141864
chr7 159138663 310249 0.0019495513796040879 1.1666384509547183
chr8 146364022 1127039 0.007700246171152635 5.11477911739867
chr9 141213431 573158 0.004058806559271264 3.133021723401934
chr10 135534747 80311 5.925491564166937E-4 0.2508745548861888
chr11 135006516 304547 0.002255794824006865 0.965930907541324
chr12 133851895 74369 5.556066277582399E-4 0.3170294448118943
chr13 115169878 2903618 0.02521160958423521 14.731825102789562
chr14 107349540 59633 5.555030790071388E-4 0.13286211353585184
chr15 102531392 246373 0.0024029031030808595 1.6696356819374498
chr16 90354753 27268 3.0178821915433714E-4 0.053373978754663355
chr17 81195210 23917 2.9456171121424525E-4 0.1004790456197398
chr18 78077248 99945 0.0012800784166982935 0.3675900573316173
chr19 59128983 11850 2.0040933225589218E-4 0.03922238088254553
chr20 63025520 41802 6.632551385533986E-4 0.11035152049285507
chr21 48129895 9310 1.9343487036487406E-4 0.04086621472701912
chr22 51304566 12080 2.3545662582936575E-4 0.056491236240594454
chrMT 16571 9114191 550.0085088407459 4631.522418035241
chrX 155270560 2343871 0.015095398638351017 9.509282046181749
chrY 59373566 4642 7.818294087304778E-5 0.01802319320898393