BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089564.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 = 11,462,968 number of mapped reads = 9,182,408 (80.1%) number of supplementary alignments = 322 (0%) number of secondary alignments = 0 number of mapped bases = 431,747,472 bp number of sequenced bases = 431,668,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,556,043 duplication rate = 19.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8561 >>>>>>> ACTG content number of A's = 137,133,538 bp (31.77%) number of C's = 82,231,399 bp (19.05%) number of T's = 117,863,235 bp (27.3%) number of G's = 93,956,997 bp (21.77%) number of N's = 482,946 bp (0.11%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 3,276,861 number of insertions = 17,176 mapped reads with insertion percentage = 0.19% number of deletions = 53,190 mapped reads with deletion percentage = 0.58% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 0.1395X std coverageData = 1.1062X There is a 5.19% of reference with a coverageData >= 1X There is a 2.41% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 33837023 0.1357550198440629 1.136338012573229 chr2 243199373 36503758 0.15009807611633932 1.2568810408567748 chr3 198022430 30179714 0.15240553304996812 1.1159415210198973 chr4 191154276 28981201 0.15161157577244047 1.128603937900282 chr5 180915260 27372060 0.15129768489402165 1.101959764287745 chr6 171115067 25265421 0.14765164425877236 1.1284982115511657 chr7 159138663 23249090 0.14609328469725802 1.140245427780479 chr8 146364022 21959343 0.1500323829581562 1.3422653311514392 chr9 141213431 17794324 0.12601013851154144 1.0129548944006637 chr10 135534747 19915402 0.14693945604959885 1.122548243671176 chr11 135006516 19667692 0.14567957593987538 1.11387876072681 chr12 133851895 20094118 0.15012202853011533 1.0872012738802264 chr13 115169878 13945387 0.12108536747777053 0.9824099007446441 chr14 107349540 13475891 0.12553282482626382 1.0762786134654532 chr15 102531392 12193073 0.11892038879175658 0.9348105799986742 chr16 90354753 11941433 0.13216164732363334 1.0611756565923842 chr17 81195210 11020326 0.13572630700751928 0.9913342347267947 chr18 78077248 11263803 0.14426485677364037 1.1077133463329323 chr19 59128983 7613435 0.12875978266022264 1.0522405290918455 chr20 63025520 8914947 0.14144979684419898 1.0553107546208422 chr21 48129895 5423511 0.11268487080638759 0.9937131451636823 chr22 51304566 4651437 0.09066321699320096 0.8096037104867365 chrMT 16571 44037 2.6574739001870737 8.130811710639211 chrX 155270560 25413124 0.16366994490133868 1.173671986502458 chrY 59373566 1027922 0.01731278865749785 0.3402487722458644