BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089754.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 = 32,322,982 number of mapped reads = 26,990,777 (83.5%) number of supplementary alignments = 1,264 (0%) number of secondary alignments = 0 number of mapped bases = 1,275,801,795 bp number of sequenced bases = 1,275,569,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,003,563 duplication rate = 12.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5243 >>>>>>> ACTG content number of A's = 392,542,506 bp (30.77%) number of C's = 253,753,784 bp (19.89%) number of T's = 366,235,353 bp (28.71%) number of G's = 262,899,538 bp (20.61%) number of N's = 137,859 bp (0.01%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 5,426,229 number of insertions = 48,652 mapped reads with insertion percentage = 0.18% number of deletions = 155,426 mapped reads with deletion percentage = 0.57% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.4121X std coverageData = 2.929X There is a 12.36% of reference with a coverageData >= 1X There is a 7.59% of reference with a coverageData >= 2X There is a 5.17% of reference with a coverageData >= 3X There is a 3.68% of reference with a coverageData >= 4X There is a 2.7% of reference with a coverageData >= 5X There is a 2.02% of reference with a coverageData >= 6X There is a 1.53% of reference with a coverageData >= 7X There is a 1.17% of reference with a coverageData >= 8X There is a 0.9% of reference with a coverageData >= 9X There is a 0.69% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.02% 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 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 100149410 0.40180204806791636 5.03671137213874 chr2 243199373 108875023 0.4476780579528879 2.767930697056548 chr3 198022430 88597381 0.4474108362370869 1.7208497704864902 chr4 191154276 86761563 0.45388240752720593 1.944071128197488 chr5 180915260 79889749 0.44158656931427454 1.7349730000726709 chr6 171115067 75437227 0.44085671894690603 1.959577151013413 chr7 159138663 69617102 0.4374619007575802 3.497830746744437 chr8 146364022 66897473 0.45706227586448805 6.197784993074919 chr9 141213431 52434667 0.37131501322986765 2.4883539029156325 chr10 135534747 59100504 0.43605426142124276 2.5487275010834507 chr11 135006516 58337068 0.4321055733339567 2.653334642512753 chr12 133851895 57789286 0.4317405143946599 1.8053082303660994 chr13 115169878 41951669 0.36425903828777173 1.55645261091341 chr14 107349540 39039442 0.36366659791928313 1.791623767074472 chr15 102531392 35037271 0.3417223770842787 1.5149615264558465 chr16 90354753 33477417 0.3705108573535694 1.7170440820703847 chr17 81195210 30306037 0.37324907466832097 1.9784821299120041 chr18 78077248 34018343 0.4357011020675319 4.368755546059109 chr19 59128983 21294816 0.3601417599216953 3.8153005126382755 chr20 63025520 25535064 0.40515435652097753 1.7325293845427283 chr21 48129895 16427975 0.34132580177039656 1.8615549058411651 chr22 51304566 12639565 0.24636335487176717 1.2493861028556612 chrMT 16571 174691 10.541970913040855 10.294902752993284 chrX 155270560 77842424 0.5013340841947115 2.1810508184673476 chrY 59373566 4170628 0.07024385228941782 1.670462954051528