BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328242.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 342,502,082 number of mapped reads = 309,530,403 (90.37%) number of supplementary alignments = 15,056,168 (4.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 156,918,575 number of mapped paired reads (second in pair) = 152,611,828 number of mapped paired reads (both in pair) = 304,244,078 number of mapped paired reads (singletons) = 5,286,325 number of mapped bases = 42,748,498,840 bp number of sequenced bases = 42,710,942,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,386,699 duplication rate = 29.94% >>>>>>> Insert size mean insert size = 172,646.5438 std insert size = 3,977,982.1831 median insert size = 323 >>>>>>> Mapping quality mean mapping quality = 53.4494 >>>>>>> ACTG content number of A's = 12,470,329,978 bp (29.2%) number of C's = 8,867,230,831 bp (20.76%) number of T's = 12,416,933,113 bp (29.07%) number of G's = 8,953,402,333 bp (20.96%) number of N's = 3,045,979 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 451,397,963 number of insertions = 7,631,456 mapped reads with insertion percentage = 2.33% number of deletions = 20,305,538 mapped reads with deletion percentage = 6.27% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 13.809X std coverageData = 155.8986X There is a 91.33% of reference with a coverageData >= 1X There is a 90.54% of reference with a coverageData >= 2X There is a 89.19% of reference with a coverageData >= 3X There is a 87.18% of reference with a coverageData >= 4X There is a 84.41% of reference with a coverageData >= 5X There is a 80.92% of reference with a coverageData >= 6X There is a 76.77% of reference with a coverageData >= 7X There is a 72.09% of reference with a coverageData >= 8X There is a 67.02% of reference with a coverageData >= 9X There is a 61.72% of reference with a coverageData >= 10X There is a 56.33% of reference with a coverageData >= 11X There is a 50.99% of reference with a coverageData >= 12X There is a 45.79% of reference with a coverageData >= 13X There is a 40.84% of reference with a coverageData >= 14X There is a 36.18% of reference with a coverageData >= 15X There is a 31.86% of reference with a coverageData >= 16X There is a 27.92% of reference with a coverageData >= 17X There is a 24.35% of reference with a coverageData >= 18X There is a 21.16% of reference with a coverageData >= 19X There is a 18.33% of reference with a coverageData >= 20X There is a 15.83% of reference with a coverageData >= 21X There is a 13.66% of reference with a coverageData >= 22X There is a 11.77% of reference with a coverageData >= 23X There is a 10.14% of reference with a coverageData >= 24X There is a 8.74% of reference with a coverageData >= 25X There is a 7.54% of reference with a coverageData >= 26X There is a 6.52% of reference with a coverageData >= 27X There is a 5.65% of reference with a coverageData >= 28X There is a 4.91% of reference with a coverageData >= 29X There is a 4.29% of reference with a coverageData >= 30X There is a 3.76% of reference with a coverageData >= 31X There is a 3.31% of reference with a coverageData >= 32X There is a 2.93% of reference with a coverageData >= 33X There is a 2.6% of reference with a coverageData >= 34X There is a 2.33% of reference with a coverageData >= 35X There is a 2.1% of reference with a coverageData >= 36X There is a 1.9% of reference with a coverageData >= 37X There is a 1.72% of reference with a coverageData >= 38X There is a 1.58% of reference with a coverageData >= 39X There is a 1.45% of reference with a coverageData >= 40X There is a 1.34% of reference with a coverageData >= 41X There is a 1.25% of reference with a coverageData >= 42X There is a 1.16% of reference with a coverageData >= 43X There is a 1.09% of reference with a coverageData >= 44X There is a 1.03% of reference with a coverageData >= 45X There is a 0.97% of reference with a coverageData >= 46X There is a 0.92% of reference with a coverageData >= 47X There is a 0.88% of reference with a coverageData >= 48X There is a 0.84% of reference with a coverageData >= 49X There is a 0.8% of reference with a coverageData >= 50X There is a 0.77% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3383812139 13.575942661342456 330.2042827826595 chr2 243199373 3585158678 14.741644412052 144.37617664362133 chr3 198022430 3132100044 15.816895308273915 19.356492969323284 chr4 191154276 2474843332 12.946837412101626 81.48331214699618 chr5 180915260 2925777941 16.172090408515015 10.818746843479733 chr6 171115067 2060426488 12.04117512340395 52.64868361181638 chr7 159138663 2935101023 18.44367024121599 87.5964915829147 chr8 146364022 2464198398 16.83609376353432 290.1405735432023 chr9 141213431 1415862574 10.02640162464433 133.84357809751427 chr10 135534747 2132069448 15.730795941206132 309.2112181217666 chr11 135006516 1498024552 11.095942598800194 49.6892333096481 chr12 133851895 2117058049 15.816421941579534 27.7566822970368 chr13 115169878 1105402802 9.598020082994271 10.240714362676476 chr14 107349540 1594055834 14.849209731126933 15.666809464303773 chr15 102531392 1344417010 13.112247710437794 14.693717048429644 chr16 90354753 1405309649 15.553245428051804 117.12608870638962 chr17 81195210 1478803781 18.212943608372957 65.75436867570698 chr18 78077248 1063542347 13.621667953768043 134.46814004584456 chr19 59128983 758737347 12.831902537542376 188.08217921956538 chr20 63025520 1460155585 23.167688025422084 46.31114984975843 chr21 48129895 493279642 10.248924125016272 42.22410035090498 chr22 51304566 393355061 7.667057567546717 12.747399602320671 chrMT 16571 298227712 17996.965300826745 4184.646917742234 chrX 155270560 1119460128 7.209738459112919 20.070081860101578 chrY 59373566 109319276 1.8412112218423937 96.91663950648196