BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975205.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,483,114 number of mapped reads = 1,795,354 (72.3%) number of supplementary alignments = 22,199 (0.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 898,461 number of mapped paired reads (second in pair) = 896,893 number of mapped paired reads (both in pair) = 1,781,384 number of mapped paired reads (singletons) = 13,970 number of mapped bases = 248,158,639 bp number of sequenced bases = 247,969,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 292,838 duplication rate = 14.26% >>>>>>> Insert size mean insert size = 65,603.5441 std insert size = 2,429,560.5248 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.3646 >>>>>>> ACTG content number of A's = 74,243,737 bp (29.94%) number of C's = 48,620,759 bp (19.61%) number of T's = 74,885,469 bp (30.2%) number of G's = 50,207,000 bp (20.25%) number of N's = 12,338 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 2,794,044 number of insertions = 54,062 mapped reads with insertion percentage = 2.84% number of deletions = 90,584 mapped reads with deletion percentage = 4.84% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.0802X std coverageData = 1.4594X There is a 4.39% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 24260325 0.09733305739687606 1.5074995447846158 chr2 243199373 17966411 0.07387523568985517 1.3412902348200015 chr3 198022430 18167125 0.09174276368591175 0.48288802660219804 chr4 191154276 14167094 0.07411340356309895 0.88254714324168 chr5 180915260 21704498 0.11997052100524853 0.506130390050538 chr6 171115067 12127424 0.0708729173451453 0.5945842431516173 chr7 159138663 10521347 0.06611433577269654 0.745912094506594 chr8 146364022 15908312 0.10869004406014478 0.643671882141509 chr9 141213431 8747328 0.06194402287414148 1.815572457732428 chr10 135534747 13063223 0.09638283384260127 5.094699213606652 chr11 135006516 9590105 0.07103438622177317 0.6895207311571493 chr12 133851895 8798729 0.06573481085194946 0.36645177466577555 chr13 115169878 5092652 0.04421861070305206 0.29616759411490406 chr14 107349540 7140063 0.06651228314532134 0.3864078059037526 chr15 102531392 5271880 0.05141722839381718 0.32342633593153947 chr16 90354753 7572483 0.08380835261649157 2.006810660790855 chr17 81195210 3906257 0.04810945128413363 0.995896792695966 chr18 78077248 6146593 0.07872450883514746 1.8196321133372795 chr19 59128983 3314862 0.056061542611006855 0.8737599963389527 chr20 63025520 3467324 0.05501460360818919 0.4521860831331475 chr21 48129895 2911435 0.06049119783037133 0.5903633926933796 chr22 51304566 1671022 0.032570629288629006 0.26352075471381325 chrMT 16571 41991 2.534005189789391 2.4830833132934265 chrX 155270560 25409573 0.16364707514418703 0.7489902491045222 chrY 59373566 1190583 0.02005240850785348 1.6663112863620213