BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124947.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,990,142 number of mapped reads = 3,901,918 (97.79%) number of supplementary alignments = 18,009 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,953,957 number of mapped paired reads (second in pair) = 1,947,961 number of mapped paired reads (both in pair) = 3,886,562 number of mapped paired reads (singletons) = 15,356 number of mapped bases = 344,246,904 bp number of sequenced bases = 344,061,282 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 280,321 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 43,649.9023 std insert size = 1,981,164.9841 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.6813 >>>>>>> ACTG content number of A's = 97,649,854 bp (28.38%) number of C's = 64,246,120 bp (18.67%) number of T's = 102,707,140 bp (29.85%) number of G's = 79,453,204 bp (23.09%) number of N's = 4,964 bp (0%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,541,213 number of insertions = 45,227 mapped reads with insertion percentage = 1.13% number of deletions = 111,631 mapped reads with deletion percentage = 2.8% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.1112X std coverageData = 1.0436X There is a 7.84% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 0.01% 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 0.01% 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% 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 30795201 0.12355115055059382 1.2224943463786808 chr2 243199373 28404304 0.11679431426823621 1.2950976426111223 chr3 198022430 31880721 0.16099550439816337 0.5589184140915637 chr4 191154276 21132394 0.11055151075982209 0.6421252669352524 chr5 180915260 20907492 0.11556511042794289 0.43626867571641736 chr6 171115067 20311324 0.11869979865653794 1.4180045206193657 chr7 159138663 18449472 0.115933310310644 1.197241497625977 chr8 146364022 24331314 0.16623835330242565 0.6425994467299241 chr9 141213431 14673144 0.10390756669597526 1.4936086426824815 chr10 135534747 16197048 0.11950476433914028 2.0712100169523344 chr11 135006516 16760105 0.12414293396031344 0.9239726387122729 chr12 133851895 13375278 0.09992595173942065 0.4005478545148788 chr13 115169878 6637399 0.057631379968988074 0.2980440920688202 chr14 107349540 11508174 0.10720282546157162 0.4914380471703943 chr15 102531392 6317881 0.061618991771807796 0.31380731925839384 chr16 90354753 9372411 0.10372903127741381 1.623935441126941 chr17 81195210 5468706 0.06735256919712382 0.7948764550782371 chr18 78077248 11330387 0.14511765322466283 1.6465308309730258 chr19 59128983 7128973 0.12056647414348391 0.8371528087257543 chr20 63025520 8088317 0.12833399867228387 0.47517267356655346 chr21 48129895 4133655 0.08588539409861584 0.44633839962658756 chr22 51304566 2999218 0.058459085298567776 0.31621248640347 chrMT 16571 73855 4.456882505582041 3.622262840650637 chrX 155270560 9924410 0.06391688160331231 0.4699153098314884 chrY 59373566 4045721 0.06814010463848508 1.2646556770208879