BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975326.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,822,330 number of mapped reads = 4,782,501 (99.17%) number of supplementary alignments = 59,144 (1.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,390,830 number of mapped paired reads (second in pair) = 2,391,671 number of mapped paired reads (both in pair) = 4,770,392 number of mapped paired reads (singletons) = 12,109 number of mapped bases = 464,682,075 bp number of sequenced bases = 464,538,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,164 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 121,558.6219 std insert size = 3,331,003.1374 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 53.2557 >>>>>>> ACTG content number of A's = 139,139,787 bp (29.95%) number of C's = 92,711,397 bp (19.96%) number of T's = 139,872,677 bp (30.11%) number of G's = 92,804,831 bp (19.98%) number of N's = 9,722 bp (0%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,297,892 number of insertions = 57,195 mapped reads with insertion percentage = 1.17% number of deletions = 62,876 mapped reads with deletion percentage = 1.28% homopolymer indels = 38.77% >>>>>>> Coverage mean coverageData = 0.1501X std coverageData = 2.3699X There is a 11.31% of reference with a coverageData >= 1X There is a 2.62% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 36492416 0.14640852589891842 4.973639784505063 chr2 243199373 40278737 0.16562023373308615 1.2322794182909131 chr3 198022430 31728734 0.16022798023436033 0.6524885832409508 chr4 191154276 34046256 0.17810878580607845 1.523673136634292 chr5 180915260 28984021 0.16020771824333668 0.47546115424127744 chr6 171115067 27618587 0.16140359516091005 0.9354406943017254 chr7 159138663 25440619 0.15986447617698032 2.085589419832251 chr8 146364022 24124568 0.16482580671361982 3.572531916198235 chr9 141213431 18992858 0.13449753232042072 1.8742562688531805 chr10 135534747 25489546 0.18806650371361966 6.448414058355809 chr11 135006516 20637374 0.15286205889499438 1.0110506870187632 chr12 133851895 20182277 0.15078065947441385 0.45899990625940273 chr13 115169878 15911705 0.13815856434266605 0.4305138680367309 chr14 107349540 13776547 0.1283335447920876 0.450719244813315 chr15 102531392 11774763 0.11484056512175315 0.392988370178657 chr16 90354753 12617591 0.13964501679286312 1.3684051047665036 chr17 81195210 10369254 0.1277077059102378 0.7333971635667248 chr18 78077248 13178165 0.16878367690418597 2.4235147547906757 chr19 59128983 7047775 0.11919323895694266 2.2789630292410705 chr20 63025520 8212481 0.13030405778484652 0.5498995322315138 chr21 48129895 6405654 0.13309096144921986 0.7243966643413658 chr22 51304566 4085370 0.07962975459143344 0.3394454267355832 chrMT 16571 525050 31.684871160461046 8.197547017626857 chrX 155270560 25398000 0.16357254073148186 0.6784661659687135 chrY 59373566 1363727 0.022968588411886866 1.2646380278902294