BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6234023.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,092,471
number of mapped reads = 876,979 (80.27%)
number of supplementary alignments = 4,295 (0.39%)
number of secondary alignments = 0
number of mapped bases = 57,489,077 bp
number of sequenced bases = 57,460,956 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 21,462
duplication rate = 1.93%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.101
>>>>>>> ACTG content
number of A's = 16,183,920 bp (28.17%)
number of C's = 9,917,661 bp (17.26%)
number of T's = 18,548,974 bp (32.28%)
number of G's = 12,799,956 bp (22.28%)
number of N's = 10,445 bp (0.02%)
GC percentage = 39.54%
>>>>>>> Mismatches and indels
general error rate = 0.0082
number of mismatches = 460,160
number of insertions = 4,436
mapped reads with insertion percentage = 0.5%
number of deletions = 16,048
mapped reads with deletion percentage = 1.81%
homopolymer indels = 45.93%
>>>>>>> Coverage
mean coverageData = 0.0186X
std coverageData = 0.1881X
There is a 1.71% of reference with a coverageData >= 1X
There is a 0.11% of reference with a coverageData >= 2X
There is a 0.01% 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 5348020 0.021456395889982556 0.26596294632430195
chr2 243199373 3883981 0.01597035778542077 0.19539879039984298
chr3 198022430 7047408 0.035588938081408256 0.2005173892170121
chr4 191154276 3148255 0.016469707431498944 0.13915234313319885
chr5 180915260 3173346 0.017540510402494516 0.14044159125343406
chr6 171115067 3795357 0.02218014501317993 0.1776761252155618
chr7 159138663 3615747 0.02272073254756451 0.25626999196936945
chr8 146364022 2648244 0.018093544874026486 0.3103217080220381
chr9 141213431 2382111 0.016868869930651283 0.1693772179605406
chr10 135534747 1031430 0.007610078026707055 0.14017774082092738
chr11 135006516 2431365 0.018009241865037093 0.1605005646420854
chr12 133851895 1902105 0.014210519768883361 0.1294767722932613
chr13 115169878 1980504 0.01719637143316241 0.13924335794899856
chr14 107349540 2681659 0.024980628701343294 0.1726243440902474
chr15 102531392 1291555 0.012596678683539184 0.11937688754781596
chr16 90354753 1286288 0.014235974946442496 0.13573320933531435
chr17 81195210 910762 0.01121694247727175 0.11604101645610267
chr18 78077248 1587217 0.020328803084862828 0.26900696531945967
chr19 59128983 1119718 0.01893687229492853 0.19126899061132385
chr20 63025520 1280896 0.02032344992948888 0.1526847264813817
chr21 48129895 1048017 0.021774761819031603 0.1597793178961635
chr22 51304566 339336 0.0066141481442411965 0.08490944846910405
chrMT 16571 11874 0.7165530143020941 0.9589522335817154
chrX 155270560 3393280 0.021853981849489047 0.1620178824269069
chrY 59373566 150602 0.0025365159977084753 0.06307630717931959