BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3083648.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,672,487
number of mapped reads = 1,285,713 (76.87%)
number of supplementary alignments = 7,891 (0.47%)
number of secondary alignments = 0
number of mapped bases = 78,770,951 bp
number of sequenced bases = 78,745,403 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 27,368
duplication rate = 1.72%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9346
>>>>>>> ACTG content
number of A's = 23,643,847 bp (30.03%)
number of C's = 15,051,903 bp (19.11%)
number of T's = 23,033,539 bp (29.25%)
number of G's = 17,005,544 bp (21.6%)
number of N's = 10,570 bp (0.01%)
GC percentage = 40.71%
>>>>>>> Mismatches and indels
general error rate = 0.0091
number of mismatches = 704,300
number of insertions = 5,748
mapped reads with insertion percentage = 0.44%
number of deletions = 16,336
mapped reads with deletion percentage = 1.26%
homopolymer indels = 45.77%
>>>>>>> Coverage
mean coverageData = 0.0254X
std coverageData = 0.2276X
There is a 2.35% of reference with a coverageData >= 1X
There is a 0.15% 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 6774949 0.027181272298615458 0.45118398263054815
chr2 243199373 8853110 0.03640268431119681 0.24150283843411774
chr3 198022430 7089836 0.03580319663787582 0.20152150575067262
chr4 191154276 3709140 0.019403908076845743 0.1480182548401325
chr5 180915260 4382743 0.02422539148991633 0.16373644221850275
chr6 171115067 5641635 0.03296983193186606 0.21233473062241512
chr7 159138663 4313481 0.027105173052760913 0.24613816524135934
chr8 146364022 5334659 0.03644788471308885 0.283419358318612
chr9 141213431 3480824 0.024649383386202123 0.18589999682672226
chr10 135534747 4245605 0.031324845428751934 0.240091607356239
chr11 135006516 2665062 0.019740247204068282 0.1655701962319988
chr12 133851895 2471228 0.018462405780657793 0.14349941780534178
chr13 115169878 2564237 0.022264823446283413 0.15705533653371642
chr14 107349540 1528663 0.01424005170399426 0.1270691513347601
chr15 102531392 2055881 0.020051234650164507 0.1491602197776116
chr16 90354753 2304104 0.02550063968411269 0.1735820343018136
chr17 81195210 1483018 0.018264845918866394 0.1460195945478322
chr18 78077248 2208234 0.028282682299458097 0.2719195846495883
chr19 59128983 1688904 0.028563048344667115 0.3124162024623764
chr20 63025520 1456319 0.023106814509424117 0.16162546768434377
chr21 48129895 1201249 0.02495847954789845 0.16886672400123773
chr22 51304566 533985 0.010408137942342207 0.10650750669569102
chrMT 16571 8583 0.517953050509927 0.7934090091121649
chrX 155270560 2628870 0.016930897911361948 0.14264422773028024
chrY 59373566 146632 0.0024696512249238996 0.06110902391961711