BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089697.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 11,237,049 number of mapped reads = 8,623,313 (76.74%) number of supplementary alignments = 61,217 (0.54%) number of secondary alignments = 0 number of mapped bases = 518,357,008 bp number of sequenced bases = 518,193,127 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 733,518 duplication rate = 5.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8304 >>>>>>> ACTG content number of A's = 153,624,920 bp (29.65%) number of C's = 101,129,538 bp (19.52%) number of T's = 146,628,235 bp (28.3%) number of G's = 116,223,246 bp (22.43%) number of N's = 587,188 bp (0.11%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 4,633,294 number of insertions = 38,825 mapped reads with insertion percentage = 0.45% number of deletions = 104,137 mapped reads with deletion percentage = 1.2% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.1674X std coverageData = 5.5159X There is a 11.24% of reference with a coverageData >= 1X There is a 3.09% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 43892424 0.17609755122736484 1.2561232061572958 chr2 243199373 51703580 0.21259750533978555 1.8857606161459437 chr3 198022430 48022404 0.24250992172957378 0.731490562886535 chr4 191154276 23725469 0.12411686254928454 1.5240261636063226 chr5 180915260 22215212 0.12279346695242845 0.4971438608147221 chr6 171115067 32153543 0.1879059720673224 13.003201817196974 chr7 159138663 32251407 0.2026622970936987 1.9010563820086712 chr8 146364022 42971440 0.293592915887485 1.401539536976786 chr9 141213431 16908293 0.11973572825378062 0.9357018978864773 chr10 135534747 21696775 0.16008274985011778 1.0301658674055365 chr11 135006516 25884963 0.1917312124401462 0.892250422986029 chr12 133851895 17562265 0.13120669677481966 15.11083806498937 chr13 115169878 15066788 0.13082229712876833 0.5010695415460963 chr14 107349540 16152940 0.15047050970129913 0.6025376285538477 chr15 102531392 14361976 0.14007393950137728 17.17575647095527 chr16 90354753 10228469 0.11320344154999792 2.9074885895216553 chr17 81195210 11764166 0.14488743855702818 0.658279206075471 chr18 78077248 25048424 0.32081591810203147 1.5648228611487178 chr19 59128983 7966264 0.13472689019528714 1.1340887026101856 chr20 63025520 11760874 0.18660494986792653 0.6676607699564749 chr21 48129895 8386654 0.17425041130881336 0.7566353427993736 chr22 51304566 3863060 0.07529661200135676 0.3878346055519979 chrMT 16571 201818 12.178987387604852 9.492930217099117 chrX 155270560 13507594 0.08699391565278054 0.6810991118413583 chrY 59373566 1060206 0.017856532316081537 1.0778311013309299