BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926995.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,681,332 number of mapped reads = 11,400,807 (97.6%) number of supplementary alignments = 269,104 (2.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,709,868 number of mapped paired reads (second in pair) = 5,690,939 number of mapped paired reads (both in pair) = 11,230,392 number of mapped paired reads (singletons) = 170,415 number of mapped bases = 1,032,477,165 bp number of sequenced bases = 1,031,691,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 739,581 duplication rate = 5.36% >>>>>>> Insert size mean insert size = 227,637.1386 std insert size = 4,668,342.749 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 52.8824 >>>>>>> ACTG content number of A's = 294,850,980 bp (28.58%) number of C's = 199,675,727 bp (19.35%) number of T's = 300,468,743 bp (29.12%) number of G's = 236,506,783 bp (22.92%) number of N's = 189,237 bp (0.02%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 9,828,783 number of insertions = 174,419 mapped reads with insertion percentage = 1.5% number of deletions = 534,379 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.87% >>>>>>> Coverage mean coverageData = 0.3335X std coverageData = 1.3805X There is a 19.66% of reference with a coverageData >= 1X There is a 7.66% of reference with a coverageData >= 2X There is a 2.96% of reference with a coverageData >= 3X There is a 1.31% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 84730630 0.3399415000855705 1.842398162884991 chr2 243199373 91886748 0.37782477342159926 2.4151112402828576 chr3 198022430 70259819 0.3548073771238945 0.8640452942071147 chr4 191154276 61460422 0.32152261140106536 1.1080141027620884 chr5 180915260 64655987 0.3573827160848676 0.8728951701625596 chr6 171115067 61330143 0.3584146275091018 1.1658300268677158 chr7 159138663 52599150 0.3305240160274565 1.0483655532791825 chr8 146364022 51252479 0.35017129414495046 0.9809011747341586 chr9 141213431 44176468 0.3128347472840597 1.553592021482696 chr10 135534747 49598344 0.36594559769975443 2.210157216126069 chr11 135006516 48892847 0.36215175717889053 1.0915395139152233 chr12 133851895 47076621 0.35170679503640945 0.8841759944680158 chr13 115169878 32558199 0.28269717364813046 0.7736115847871936 chr14 107349540 30099019 0.2803833067193395 0.7860490128998117 chr15 102531392 29616280 0.2888508526247259 0.7916173810916948 chr16 90354753 31225240 0.3455849190357479 1.79077196641008 chr17 81195210 25247845 0.3109523948518638 1.0060822547892287 chr18 78077248 26684794 0.3417742643798101 1.5476896273917842 chr19 59128983 16051618 0.2714678518992962 1.2341153048851123 chr20 63025520 23543520 0.37355534710383986 0.9479687680176218 chr21 48129895 12700947 0.2638889405430866 1.2618936992513679 chr22 51304566 12916945 0.2517698912022762 0.7983244892757462 chrMT 16571 156074 9.418502202643172 9.036125920505647 chrX 155270560 61681820 0.3972538000764601 0.9943437404329496 chrY 59373566 2075206 0.03495168203304481 1.4118443024167735