BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354884.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 18,330,356 number of mapped reads = 17,830,243 (97.27%) number of supplementary alignments = 668,142 (3.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,934,911 number of mapped paired reads (second in pair) = 8,895,332 number of mapped paired reads (both in pair) = 17,755,348 number of mapped paired reads (singletons) = 74,895 number of mapped bases = 2,500,133,150 bp number of sequenced bases = 2,498,052,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,738,352 duplication rate = 52.61% >>>>>>> Insert size mean insert size = 281,097.0889 std insert size = 5,899,452.4684 median insert size = 295 >>>>>>> Mapping quality mean mapping quality = 53.5643 >>>>>>> ACTG content number of A's = 674,816,793 bp (27.01%) number of C's = 556,577,905 bp (22.28%) number of T's = 669,111,801 bp (26.79%) number of G's = 597,533,774 bp (23.92%) number of N's = 11,750 bp (0%) GC percentage = 46.2% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 29,908,428 number of insertions = 559,043 mapped reads with insertion percentage = 3.04% number of deletions = 1,338,576 mapped reads with deletion percentage = 7.2% homopolymer indels = 51.84% >>>>>>> Coverage mean coverageData = 0.8076X std coverageData = 19.043X There is a 17.1% of reference with a coverageData >= 1X There is a 13.06% of reference with a coverageData >= 2X There is a 9.53% of reference with a coverageData >= 3X There is a 7.53% of reference with a coverageData >= 4X There is a 5.71% of reference with a coverageData >= 5X There is a 4.63% of reference with a coverageData >= 6X There is a 3.62% of reference with a coverageData >= 7X There is a 2.98% of reference with a coverageData >= 8X There is a 2.4% of reference with a coverageData >= 9X There is a 1.99% of reference with a coverageData >= 10X There is a 1.63% of reference with a coverageData >= 11X There is a 1.37% of reference with a coverageData >= 12X There is a 1.14% of reference with a coverageData >= 13X There is a 0.97% of reference with a coverageData >= 14X There is a 0.81% of reference with a coverageData >= 15X There is a 0.69% of reference with a coverageData >= 16X There is a 0.59% of reference with a coverageData >= 17X There is a 0.5% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 226156754 0.9073468025582171 3.1240712549287433 chr2 243199373 220427432 0.9063651327752396 66.0456478943081 chr3 198022430 161025046 0.8131656903715402 2.7369172406018527 chr4 191154276 129342448 0.6766390514853039 2.815131894673964 chr5 180915260 140340653 0.7757259006233084 2.662490597478889 chr6 171115067 133446629 0.7798648671890477 2.6512577235708785 chr7 159138663 130830682 0.8221175139569948 13.071608184326404 chr8 146364022 121222366 0.8282251631483589 2.772301104500872 chr9 141213431 108523305 0.7685055467563847 2.9055591376189582 chr10 135534747 123140832 0.9085554422438993 3.088986862027983 chr11 135006516 130407503 0.9659348812467689 3.2722371168305484 chr12 133851895 115696865 0.864364789157449 2.8663693100687353 chr13 115169878 65265591 0.56668976414128 2.268640969002377 chr14 107349540 76160716 0.7094647634260939 8.6184909341089 chr15 102531392 80750599 0.7875695182213073 2.7720070848914826 chr16 90354753 89632470 0.9920061427205716 3.342324089523068 chr17 81195210 86449409 1.0647107015302997 3.699702801867105 chr18 78077248 65306874 0.8364392402765015 8.156576447859527 chr19 59128983 62971790 1.0649902434479552 3.3460550480489526 chr20 63025520 69646449 1.1050515568931443 3.3123078305821965 chr21 48129895 30919482 0.6424173998301888 2.915323163968137 chr22 51304566 47343906 0.9228010232071742 3.0938170504475937 chrMT 16571 305098 18.411562367992275 13.180245058719095 chrX 155270560 68234313 0.4394542854743359 1.7661279563323484 chrY 59373566 16585938 0.27934886040026635 4.117143330417527