BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617667.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,139,578 (94.19%) number of supplementary alignments = 144,400 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,155,286 number of mapped paired reads (second in pair) = 14,984,292 number of mapped paired reads (both in pair) = 29,544,598 number of mapped paired reads (singletons) = 594,980 number of mapped bases = 2,925,979,784 bp number of sequenced bases = 2,924,215,416 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,861,502 duplication rate = 10.61% >>>>>>> Insert size mean insert size = 32,983.6173 std insert size = 1,659,685.9352 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.6314 >>>>>>> ACTG content number of A's = 872,712,981 bp (29.84%) number of C's = 581,719,351 bp (19.89%) number of T's = 869,980,277 bp (29.75%) number of G's = 597,662,155 bp (20.44%) number of N's = 2,140,652 bp (0.07%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0157 number of mismatches = 44,983,992 number of insertions = 453,978 mapped reads with insertion percentage = 1.48% number of deletions = 1,068,257 mapped reads with deletion percentage = 3.47% homopolymer indels = 47.6% >>>>>>> Coverage mean coverageData = 0.9452X std coverageData = 10.7013X There is a 33.23% of reference with a coverageData >= 1X There is a 19.23% of reference with a coverageData >= 2X There is a 11.74% of reference with a coverageData >= 3X There is a 7.49% of reference with a coverageData >= 4X There is a 4.93% of reference with a coverageData >= 5X There is a 3.33% of reference with a coverageData >= 6X There is a 2.31% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 178990164 0.7181132118423087 10.246989652486464 chr2 243199373 302583623 1.2441792890642034 12.206263462945893 chr3 198022430 245036216 1.2374164684273392 2.4716218710013496 chr4 191154276 163986848 0.8578769537962101 8.2787207648122 chr5 180915260 193723136 1.0707948903812758 2.320466558372299 chr6 171115067 141805615 0.8287149547152385 5.7464121372674954 chr7 159138663 229203854 1.4402776150004477 13.556475778452711 chr8 146364022 130263227 0.8899948581626159 4.094793104968454 chr9 141213431 120128940 0.8506906117166716 20.668366106768296 chr10 135534747 124156730 0.9160509223512994 21.886234494328537 chr11 135006516 160871001 1.191579530872421 12.092255114590978 chr12 133851895 124988706 0.9337836121035119 2.1535904211687082 chr13 115169878 126044391 1.0944215031642215 2.2876308619496433 chr14 107349540 83536851 0.778176143092928 2.4423105311971303 chr15 102531392 62351827 0.6081242611043455 1.5761625761099638 chr16 90354753 81379755 0.9006693316952568 17.058610082660245 chr17 81195210 71533372 0.8810048277478437 12.904118210983237 chr18 78077248 54070215 0.6925220391989226 18.4569294450311 chr19 59128983 30791707 0.5207548893577283 6.032303551854128 chr20 63025520 78604891 1.2471914710104732 2.9906164477371133 chr21 48129895 42801594 0.8892933175939819 4.402600564445254 chr22 51304566 18724405 0.3649656640697438 1.2692276319973494 chrMT 16571 3058360 184.5609800253455 129.02229998574697 chrX 155270560 145523155 0.9372230962521163 4.348325318945431 chrY 59373566 11821201 0.19909872012740484 17.535980701195683