BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354867.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 = 20,485,170 number of mapped reads = 20,168,237 (98.45%) number of supplementary alignments = 781,469 (3.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,092,610 number of mapped paired reads (second in pair) = 10,075,627 number of mapped paired reads (both in pair) = 20,129,266 number of mapped paired reads (singletons) = 38,971 number of mapped bases = 2,578,322,573 bp number of sequenced bases = 2,577,051,656 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,961,229 duplication rate = 54.23% >>>>>>> Insert size mean insert size = 339,899.1122 std insert size = 6,712,907.2595 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 53.7758 >>>>>>> ACTG content number of A's = 722,219,840 bp (28.03%) number of C's = 544,553,036 bp (21.13%) number of T's = 731,752,804 bp (28.39%) number of G's = 578,484,240 bp (22.45%) number of N's = 41,736 bp (0%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 15,134,947 number of insertions = 427,663 mapped reads with insertion percentage = 1.98% number of deletions = 452,821 mapped reads with deletion percentage = 2.14% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.8329X std coverageData = 37.0562X There is a 26.9% of reference with a coverageData >= 1X There is a 20.06% of reference with a coverageData >= 2X There is a 10.81% of reference with a coverageData >= 3X There is a 8.07% of reference with a coverageData >= 4X There is a 4.25% of reference with a coverageData >= 5X There is a 3.21% of reference with a coverageData >= 6X There is a 1.69% of reference with a coverageData >= 7X There is a 1.28% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 210734713 0.8454731713587185 23.67260654870539 chr2 243199373 247306064 1.0168861085016037 125.06490107256958 chr3 198022430 166283117 0.8397185965246462 2.0525045086584695 chr4 191154276 170342029 0.891123298753725 10.995867914648027 chr5 180915260 149667961 0.827282126449698 1.8308970154335968 chr6 171115067 142653145 0.8336679376106606 3.348060096681581 chr7 159138663 140488802 0.8828074796631916 28.511838351259993 chr8 146364022 127083839 0.8682723886885262 6.238732213727114 chr9 141213431 111328930 0.7883735223457604 13.262401007405023 chr10 135534747 139658863 1.0304284775032635 23.991509186753824 chr11 135006516 117121306 0.8675233571689236 4.773652067219411 chr12 133851895 115933584 0.8661333035292478 1.8599248675000035 chr13 115169878 78605079 0.6825142160869528 1.6085062919719837 chr14 107349540 77700661 0.7238099110624974 3.171199579963171 chr15 102531392 72752721 0.7095653300015667 1.648287165835476 chr16 90354753 80616068 0.8922172362089241 4.8608237093420605 chr17 81195210 74825519 0.9215509018327559 5.241054845576956 chr18 78077248 70814919 0.9069853358560999 10.932838043785232 chr19 59128983 54723280 0.9254899581141113 12.488053118768859 chr20 63025520 56454113 0.8957341883097514 3.7007003407556236 chr21 48129895 35698723 0.7417162036193929 5.761679612891156 chr22 51304566 34565202 0.6737256485124541 2.8950763481277475 chrMT 16571 2902910 175.18013396898195 36.15443390576466 chrX 155270560 71572146 0.4609511680771938 2.0282507055159353 chrY 59373566 28488879 0.4798242874615279 13.399449391290512