BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094037.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 349,286 number of mapped reads = 309,049 (88.48%) number of supplementary alignments = 11,053 (3.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 155,073 number of mapped paired reads (second in pair) = 153,976 number of mapped paired reads (both in pair) = 306,686 number of mapped paired reads (singletons) = 2,363 number of mapped bases = 39,402,655 bp number of sequenced bases = 38,366,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,828 duplication rate = 51.06% >>>>>>> Insert size mean insert size = 505,178.5633 std insert size = 6,431,823.5398 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 41.7984 >>>>>>> ACTG content number of A's = 10,554,686 bp (27.51%) number of C's = 8,607,170 bp (22.43%) number of T's = 10,177,953 bp (26.53%) number of G's = 9,026,008 bp (23.53%) number of N's = 362 bp (0%) GC percentage = 45.96% >>>>>>> Mismatches and indels general error rate = 0.0461 number of mismatches = 1,716,097 number of insertions = 28,203 mapped reads with insertion percentage = 8.96% number of deletions = 147,078 mapped reads with deletion percentage = 44.28% homopolymer indels = 26.55% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 3.5161X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% 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% 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 685424 0.002749938986109888 0.9668059319574748 chr2 243199373 1234678 0.005076814075503393 1.754409638891377 chr3 198022430 1169828 0.005907552997910388 1.9900354465472139 chr4 191154276 804715 0.004209767193489305 1.6518785332827433 chr5 180915260 366765 0.002027275090006227 0.6474039987413468 chr6 171115067 1677386 0.009802678568334371 5.0928026782805444 chr7 159138663 980089 0.0061587107841920225 2.649254620796467 chr8 146364022 889476 0.0060771492054242674 2.7842975083027386 chr9 141213431 540924 0.0038305421528919584 1.5611846128881828 chr10 135534747 672850 0.004964409606342497 1.7087134216600832 chr11 135006516 1180184 0.008741681771863515 2.9797149448698064 chr12 133851895 1062526 0.007938072150566116 2.001390523882004 chr13 115169878 586251 0.005090315368745984 2.015739950787933 chr14 107349540 163221 0.0015204629661198362 0.5458814661751507 chr15 102531392 381096 0.003716871414366441 1.1276934796115377 chr16 90354753 230155 0.002547237332384717 0.8093185582477973 chr17 81195210 977335 0.012036855376074525 2.9374445432682132 chr18 78077248 192589 0.002466646877717821 0.9339741799353096 chr19 59128983 163546 0.0027659193800103074 0.7669632115791546 chr20 63025520 150531 0.002388413455374902 0.5271206537628585 chr21 48129895 142263 0.002955813637241469 0.8486003736079593 chr22 51304566 44599 8.692988456427056E-4 0.21808286060100388 chrMT 16571 2355676 142.1565385311689 584.0003146311439 chrX 155270560 22384763 0.14416617676911836 11.072599479402387 chrY 59373566 365785 0.006160738265240798 1.695310736106456