BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695925.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 389,435,188 number of mapped reads = 387,273,556 (99.44%) number of supplementary alignments = 3,437,146 (0.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 194,293,272 number of mapped paired reads (second in pair) = 192,980,284 number of mapped paired reads (both in pair) = 385,676,322 number of mapped paired reads (singletons) = 1,597,234 number of mapped bases = 38,499,658,250 bp number of sequenced bases = 38,491,970,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,103,190 duplication rate = 16.11% >>>>>>> Insert size mean insert size = 41,688.7457 std insert size = 1,945,246.4001 median insert size = 310 >>>>>>> Mapping quality mean mapping quality = 54.5076 >>>>>>> ACTG content number of A's = 11,628,037,642 bp (30.21%) number of C's = 7,574,316,669 bp (19.68%) number of T's = 11,624,237,184 bp (30.2%) number of G's = 7,658,653,289 bp (19.9%) number of N's = 6,726,002 bp (0.02%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 133,772,334 number of insertions = 2,636,694 mapped reads with insertion percentage = 0.67% number of deletions = 3,506,014 mapped reads with deletion percentage = 0.89% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 12.4365X std coverageData = 16.6807X There is a 85.94% of reference with a coverageData >= 1X There is a 80.6% of reference with a coverageData >= 2X There is a 75.44% of reference with a coverageData >= 3X There is a 70.43% of reference with a coverageData >= 4X There is a 65.6% of reference with a coverageData >= 5X There is a 60.99% of reference with a coverageData >= 6X There is a 56.6% of reference with a coverageData >= 7X There is a 52.46% of reference with a coverageData >= 8X There is a 48.56% of reference with a coverageData >= 9X There is a 44.92% of reference with a coverageData >= 10X There is a 41.52% of reference with a coverageData >= 11X There is a 38.36% of reference with a coverageData >= 12X There is a 35.43% of reference with a coverageData >= 13X There is a 32.72% of reference with a coverageData >= 14X There is a 30.22% of reference with a coverageData >= 15X There is a 27.91% of reference with a coverageData >= 16X There is a 25.78% of reference with a coverageData >= 17X There is a 23.82% of reference with a coverageData >= 18X There is a 22.02% of reference with a coverageData >= 19X There is a 20.36% of reference with a coverageData >= 20X There is a 18.84% of reference with a coverageData >= 21X There is a 17.44% of reference with a coverageData >= 22X There is a 16.16% of reference with a coverageData >= 23X There is a 14.97% of reference with a coverageData >= 24X There is a 13.89% of reference with a coverageData >= 25X There is a 12.89% of reference with a coverageData >= 26X There is a 11.97% of reference with a coverageData >= 27X There is a 11.12% of reference with a coverageData >= 28X There is a 10.34% of reference with a coverageData >= 29X There is a 9.63% of reference with a coverageData >= 30X There is a 8.96% of reference with a coverageData >= 31X There is a 8.35% of reference with a coverageData >= 32X There is a 7.79% of reference with a coverageData >= 33X There is a 7.27% of reference with a coverageData >= 34X There is a 6.79% of reference with a coverageData >= 35X There is a 6.35% of reference with a coverageData >= 36X There is a 5.94% of reference with a coverageData >= 37X There is a 5.56% of reference with a coverageData >= 38X There is a 5.2% of reference with a coverageData >= 39X There is a 4.88% of reference with a coverageData >= 40X There is a 4.58% of reference with a coverageData >= 41X There is a 4.3% of reference with a coverageData >= 42X There is a 4.04% of reference with a coverageData >= 43X There is a 3.79% of reference with a coverageData >= 44X There is a 3.57% of reference with a coverageData >= 45X There is a 3.36% of reference with a coverageData >= 46X There is a 3.17% of reference with a coverageData >= 47X There is a 2.98% of reference with a coverageData >= 48X There is a 2.82% of reference with a coverageData >= 49X There is a 2.66% of reference with a coverageData >= 50X There is a 2.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3019466097 12.114176826865359 19.07275785480895 chr2 243199373 3604789919 14.822365183482606 17.13197095235931 chr3 198022430 2943864111 14.86631646223107 16.137598405078805 chr4 191154276 2849089320 14.904659103728342 15.508727501528762 chr5 180915260 2569643407 14.203574684634122 15.756193820140739 chr6 171115067 2575799810 15.053027504585554 18.463919838206394 chr7 159138663 2071573939 13.017414498449066 15.595219541013774 chr8 146364022 2293618003 15.6706407193429 19.251928173940644 chr9 141213431 1556212774 11.020288672116465 16.18228765572602 chr10 135534747 1758043774 12.971166530454363 17.091035823693765 chr11 135006516 1767359042 13.090916604351156 15.57403815511854 chr12 133851895 1901651972 14.207135222104998 18.08281337001287 chr13 115169878 1303657800 11.319433715124713 15.36567674044842 chr14 107349540 1303420821 12.141838903082398 16.584904439161534 chr15 102531392 1030785140 10.053361413448869 14.666967673788847 chr16 90354753 985188897 10.903564718947326 18.40193981959798 chr17 81195210 711082889 8.75769505368605 14.821773971752558 chr18 78077248 1065995959 13.653093395402461 16.887721910122842 chr19 59128983 327860156 5.544829952512459 13.812253920333902 chr20 63025520 684481862 10.860392139565052 15.136530834751694 chr21 48129895 465503053 9.67180695075275 19.915501817492803 chr22 51304566 260894681 5.085213682540458 11.41793840711101 chrMT 16571 1823668 110.05177720113451 47.282022561767185 chrX 155270560 1233041465 7.941244399453445 11.824701050631727 chrY 59373566 214809691 3.6179348062065197 9.814126953466417