BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960920.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 228,325,396 number of mapped reads = 223,580,206 (97.92%) number of supplementary alignments = 461,959 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 112,279,767 number of mapped paired reads (second in pair) = 111,300,439 number of mapped paired reads (both in pair) = 221,628,616 number of mapped paired reads (singletons) = 1,951,590 number of mapped bases = 21,832,269,583 bp number of sequenced bases = 21,825,988,459 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,010,459 duplication rate = 12.21% >>>>>>> Insert size mean insert size = 19,048.8366 std insert size = 1,285,248.8609 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5704 >>>>>>> ACTG content number of A's = 6,677,597,126 bp (30.59%) number of C's = 4,246,010,635 bp (19.45%) number of T's = 6,675,955,771 bp (30.59%) number of G's = 4,224,377,924 bp (19.35%) number of N's = 2,047,003 bp (0.01%) GC percentage = 38.81% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 310,606,644 number of insertions = 2,644,558 mapped reads with insertion percentage = 1.15% number of deletions = 2,904,422 mapped reads with deletion percentage = 1.26% homopolymer indels = 40.22% >>>>>>> Coverage mean coverageData = 7.0525X std coverageData = 104.5375X There is a 89.47% of reference with a coverageData >= 1X There is a 85.3% of reference with a coverageData >= 2X There is a 79.16% of reference with a coverageData >= 3X There is a 71.51% of reference with a coverageData >= 4X There is a 62.95% of reference with a coverageData >= 5X There is a 54.1% of reference with a coverageData >= 6X There is a 45.49% of reference with a coverageData >= 7X There is a 37.5% of reference with a coverageData >= 8X There is a 30.37% of reference with a coverageData >= 9X There is a 24.23% of reference with a coverageData >= 10X There is a 19.08% of reference with a coverageData >= 11X There is a 14.86% of reference with a coverageData >= 12X There is a 11.48% of reference with a coverageData >= 13X There is a 8.8% of reference with a coverageData >= 14X There is a 6.72% of reference with a coverageData >= 15X There is a 5.12% of reference with a coverageData >= 16X There is a 3.9% of reference with a coverageData >= 17X There is a 2.97% of reference with a coverageData >= 18X There is a 2.28% of reference with a coverageData >= 19X There is a 1.76% of reference with a coverageData >= 20X There is a 1.37% of reference with a coverageData >= 21X There is a 1.08% of reference with a coverageData >= 22X There is a 0.86% of reference with a coverageData >= 23X There is a 0.7% of reference with a coverageData >= 24X There is a 0.58% of reference with a coverageData >= 25X There is a 0.5% of reference with a coverageData >= 26X There is a 0.43% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.34% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1814681409 7.280549198711926 276.98505282457154 chr2 243199373 1838493551 7.559614682888183 56.100078780083365 chr3 198022430 1622368987 8.192854652879474 9.720428484837015 chr4 191154276 1440981088 7.538314696135806 57.06234106059795 chr5 180915260 1186091877 6.5560631922370725 9.48202140622197 chr6 171115067 1147192448 6.704216455702291 27.501565692337458 chr7 159138663 1201576369 7.550499334030474 68.82552620351366 chr8 146364022 1279765246 8.74371466780272 131.5241854168973 chr9 141213431 931818918 6.598656454994002 99.18359955419052 chr10 135534747 1041614101 7.68521817508539 201.03173944478664 chr11 135006516 1064801479 7.887037681944181 43.99366273640421 chr12 133851895 986463680 7.369814824063567 11.722574934951803 chr13 115169878 753256337 6.540393634870395 4.882085306549982 chr14 107349540 464570861 4.327646499463342 7.406089897379244 chr15 102531392 586811508 5.723237503690577 5.172170530407974 chr16 90354753 716908101 7.9343706578446405 86.3210229332218 chr17 81195210 416286903 5.126988439342665 26.45342214178632 chr18 78077248 838556347 10.74008585702201 102.25489750732193 chr19 59128983 403213045 6.819211570068776 116.59621292737108 chr20 63025520 410553210 6.514078900102689 18.892694353640195 chr21 48129895 291261878 6.051579335462917 23.018035085912175 chr22 51304566 224891137 4.383452673588546 5.651723045864021 chrMT 16571 4968570 299.83525436002657 59.754898855855494 chrX 155270560 1104981653 7.116491709696931 29.56283672827484 chrY 59373566 60160880 1.0132603455214397 53.25915182822809