BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818861.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,003,130
number of mapped reads = 981,603 (97.85%)
number of supplementary alignments = 16,356 (1.63%)
number of secondary alignments = 0
number of mapped bases = 90,754,525 bp
number of sequenced bases = 90,695,741 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 173,347
duplication rate = 14.89%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.3761
>>>>>>> ACTG content
number of A's = 25,401,381 bp (28.01%)
number of C's = 18,627,239 bp (20.54%)
number of T's = 26,494,637 bp (29.21%)
number of G's = 20,171,184 bp (22.24%)
number of N's = 1,300 bp (0%)
GC percentage = 42.78%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 564,312
number of insertions = 11,819
mapped reads with insertion percentage = 1.16%
number of deletions = 30,139
mapped reads with deletion percentage = 3%
homopolymer indels = 42.43%
>>>>>>> Coverage
mean coverageData = 0.0293X
std coverageData = 0.3931X
There is a 2.22% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.11% of reference with a coverageData >= 3X
There is a 0.04% 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 8675755 0.03480735560534471 0.6048460747849722
chr2 243199373 6948469 0.02857108106113415 0.5759511847873586
chr3 198022430 5663224 0.028598901649676756 0.21079463547867022
chr4 191154276 4673799 0.02445040256384325 0.2618966643459629
chr5 180915260 4055900 0.022418783246919028 0.19494254364651709
chr6 171115067 4504156 0.026322381067705746 0.21733025977945172
chr7 159138663 7654250 0.04809799112111429 0.7785475398075967
chr8 146364022 7944000 0.054275633393020585 0.3529389532647732
chr9 141213431 3328081 0.02356773698105246 0.30441520582615106
chr10 135534747 4280047 0.031578964765397025 0.529734171657997
chr11 135006516 3998495 0.029617051965106632 0.25731433888940425
chr12 133851895 3548491 0.026510577231648458 0.20566687106986686
chr13 115169878 2775172 0.024096335328235737 0.19467200765617051
chr14 107349540 2630052 0.024499890730784686 0.20717194448634008
chr15 102531392 2504154 0.024423290771279103 0.19258438606029418
chr16 90354753 2305499 0.025516078827640645 0.3962855582523609
chr17 81195210 2186416 0.026927893899159814 0.23922702519132444
chr18 78077248 1755213 0.02248046703695294 0.35897774500547996
chr19 59128983 1556438 0.026322759517105172 0.47506081451487897
chr20 63025520 3869705 0.06139901741389837 0.32772139618601587
chr21 48129895 892920 0.018552294784769423 0.21192680506192396
chr22 51304566 826364 0.016107026419441887 0.16829539207537345
chrMT 16571 145149 8.759217910808038 6.505674242818687
chrX 155270560 3646247 0.023483183161057703 0.21522443380122996
chrY 59373566 386529 0.006510119334924232 0.493933914372546