BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975283.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 = 52,525,372 number of mapped reads = 52,255,052 (99.49%) number of supplementary alignments = 129,791 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,208,266 number of mapped paired reads (second in pair) = 26,046,786 number of mapped paired reads (both in pair) = 52,035,726 number of mapped paired reads (singletons) = 219,326 number of mapped bases = 4,957,667,759 bp number of sequenced bases = 4,955,827,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,227,599 duplication rate = 59.1% >>>>>>> Insert size mean insert size = 114,270.53 std insert size = 3,330,953.2963 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 56.2126 >>>>>>> ACTG content number of A's = 1,316,983,066 bp (26.57%) number of C's = 1,123,797,308 bp (22.68%) number of T's = 1,336,049,073 bp (26.96%) number of G's = 1,177,951,879 bp (23.77%) number of N's = 1,046,498 bp (0.02%) GC percentage = 46.45% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 41,548,043 number of insertions = 608,329 mapped reads with insertion percentage = 1.15% number of deletions = 1,257,724 mapped reads with deletion percentage = 2.37% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 1.6015X std coverageData = 27.2698X There is a 7.78% of reference with a coverageData >= 1X There is a 4.89% of reference with a coverageData >= 2X There is a 2.96% of reference with a coverageData >= 3X There is a 2.36% of reference with a coverageData >= 4X There is a 1.99% of reference with a coverageData >= 5X There is a 1.8% of reference with a coverageData >= 6X There is a 1.66% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.49% of reference with a coverageData >= 9X There is a 1.42% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.32% of reference with a coverageData >= 12X There is a 1.28% of reference with a coverageData >= 13X There is a 1.24% of reference with a coverageData >= 14X There is a 1.2% of reference with a coverageData >= 15X There is a 1.17% of reference with a coverageData >= 16X There is a 1.13% of reference with a coverageData >= 17X There is a 1.1% of reference with a coverageData >= 18X There is a 1.08% of reference with a coverageData >= 19X There is a 1.05% of reference with a coverageData >= 20X There is a 1.03% of reference with a coverageData >= 21X There is a 1% of reference with a coverageData >= 22X There is a 0.98% of reference with a coverageData >= 23X There is a 0.96% of reference with a coverageData >= 24X There is a 0.94% of reference with a coverageData >= 25X There is a 0.92% of reference with a coverageData >= 26X There is a 0.91% of reference with a coverageData >= 27X There is a 0.89% of reference with a coverageData >= 28X There is a 0.87% of reference with a coverageData >= 29X There is a 0.86% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.81% of reference with a coverageData >= 33X There is a 0.8% of reference with a coverageData >= 34X There is a 0.78% of reference with a coverageData >= 35X There is a 0.77% of reference with a coverageData >= 36X There is a 0.76% of reference with a coverageData >= 37X There is a 0.75% of reference with a coverageData >= 38X There is a 0.74% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.7% of reference with a coverageData >= 42X There is a 0.69% of reference with a coverageData >= 43X There is a 0.68% of reference with a coverageData >= 44X There is a 0.67% of reference with a coverageData >= 45X There is a 0.66% of reference with a coverageData >= 46X There is a 0.65% of reference with a coverageData >= 47X There is a 0.65% of reference with a coverageData >= 48X There is a 0.64% of reference with a coverageData >= 49X There is a 0.63% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 609812845 2.4465850578562853 34.70355090131071 chr2 243199373 355413330 1.4614072627563888 23.121904287895084 chr3 198022430 327412893 1.6534131663771625 25.900663380959912 chr4 191154276 127129333 0.6650614135359442 13.261265628984592 chr5 180915260 243306927 1.3448668011753127 23.63311156558212 chr6 171115067 468889168 2.740198021253149 46.894221102848 chr7 159138663 255760230 1.6071533163502825 26.8423140572546 chr8 146364022 160028264 1.0933579291774314 18.96062435667458 chr9 141213431 205560429 1.4556719395905053 24.676727061845213 chr10 135534747 196973682 1.4533076304041797 21.174274333402497 chr11 135006516 244363450 1.8100122663709062 26.681113849422275 chr12 133851895 278381544 2.079772901235354 33.48962493667761 chr13 115169878 103324799 0.8971512412299334 22.554698104228212 chr14 107349540 159109803 1.482165671133756 23.70304225901034 chr15 102531392 180622306 1.7616293164146255 27.833828312165146 chr16 90354753 155208598 1.7177690475231557 24.747975420366963 chr17 81195210 193096806 2.378179771934822 31.99492630429294 chr18 78077248 82203121 1.0528434736839085 18.018626637319855 chr19 59128983 205791623 3.4803849577456796 47.61223978401484 chr20 63025520 136377529 2.1638461531138495 32.47673764697185 chr21 48129895 43837648 0.9108195228765822 15.661981400935048 chr22 51304566 85942717 1.6751475297539793 26.560319059991162 chrMT 16571 60063 3.624585118580653 8.27784982671714 chrX 155270560 129014540 0.8309014922081817 18.510508353306683 chrY 59373566 10046111 0.16920174543668137 6.735125156546401