BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714173.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 = 921,010
number of mapped reads = 871,974 (94.68%)
number of supplementary alignments = 37,288 (4.05%)
number of secondary alignments = 0
number of mapped bases = 112,111,840 bp
number of sequenced bases = 109,781,482 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 824,018
duplication rate = 40.98%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.8553
>>>>>>> ACTG content
number of A's = 32,866,976 bp (29.94%)
number of C's = 22,045,687 bp (20.08%)
number of T's = 30,853,258 bp (28.1%)
number of G's = 24,014,926 bp (21.88%)
number of N's = 635 bp (0%)
GC percentage = 41.96%
>>>>>>> Mismatches and indels
general error rate = 0.0449
number of mismatches = 4,464,603
number of insertions = 135,479
mapped reads with insertion percentage = 15.09%
number of deletions = 378,034
mapped reads with deletion percentage = 41.33%
homopolymer indels = 25%
>>>>>>> Coverage
mean coverageData = 0.0362X
std coverageData = 12.741X
There is a 0.06% of reference with a coverageData >= 1X
There is a 0.04% 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 0.01% 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 10186593 0.040868877113048395 21.01139460738521
chr2 243199373 9498068 0.0390546566088392 10.299016405982766
chr3 198022430 4655965 0.023512311206361824 6.995684439179837
chr4 191154276 10935986 0.057210260888958614 15.686443576805422
chr5 180915260 4926903 0.02723320851983409 6.4590316931585505
chr6 171115067 5986284 0.03498396783493063 8.380440568601468
chr7 159138663 8228401 0.051705857300057875 17.274755137004526
chr8 146364022 6500916 0.04441607924657878 12.471777931342693
chr9 141213431 2865014 0.02028853756835637 4.126517975036246
chr10 135534747 3343963 0.024672366858072198 3.8173056256428537
chr11 135006516 3290443 0.02437247547370232 8.39534307968571
chr12 133851895 2608710 0.019489526091505838 4.243176421332376
chr13 115169878 3083717 0.02677537784662757 4.935903490753564
chr14 107349540 4341043 0.040438394053668045 22.903774988832257
chr15 102531392 2698769 0.026321392379028658 6.948199718141137
chr16 90354753 3294670 0.036463715417383746 10.70784788449549
chr17 81195210 676551 0.008332400396525854 1.136035547325207
chr18 78077248 4658772 0.059668752669151455 19.791270406434354
chr19 59128983 210245 0.0035557012708978945 0.569786210727227
chr20 63025520 2717684 0.043120374096080445 18.918712272479233
chr21 48129895 2177140 0.04523467171494972 22.639911490639683
chr22 51304566 371235 0.0072359056696824995 1.3891867570418008
chrMT 16571 2379 0.1435640576911472 1.338893279551838
chrX 155270560 14592221 0.09397931584712517 18.18214296371697
chrY 59373566 260168 0.004381882671490542 0.8834196890929762