BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 11,689,736 number of mapped reads = 11,368,805 (97.25%) number of supplementary alignments = 1,168,731 (10%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,689,660 number of mapped paired reads (second in pair) = 5,679,145 number of mapped paired reads (both in pair) = 11,149,698 number of mapped paired reads (singletons) = 219,107 number of mapped bases = 1,341,692,964 bp number of sequenced bases = 1,340,936,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,219,258 duplication rate = 66.76% >>>>>>> Insert size mean insert size = 1,016,064.9692 std insert size = 8,754,692.9942 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.6257 >>>>>>> ACTG content number of A's = 404,855,639 bp (30.19%) number of C's = 261,202,110 bp (19.48%) number of T's = 404,156,801 bp (30.14%) number of G's = 270,705,928 bp (20.19%) number of N's = 16,419 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 13,663,631 number of insertions = 141,901 mapped reads with insertion percentage = 1.2% number of deletions = 306,851 mapped reads with deletion percentage = 2.63% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.4334X std coverageData = 6.3483X There is a 7.71% of reference with a coverageData >= 1X There is a 6.31% of reference with a coverageData >= 2X There is a 5.08% of reference with a coverageData >= 3X There is a 4.32% of reference with a coverageData >= 4X There is a 3.46% of reference with a coverageData >= 5X There is a 2.89% of reference with a coverageData >= 6X There is a 2.25% of reference with a coverageData >= 7X There is a 1.87% of reference with a coverageData >= 8X There is a 1.45% of reference with a coverageData >= 9X There is a 1.22% of reference with a coverageData >= 10X There is a 0.94% of reference with a coverageData >= 11X There is a 0.81% of reference with a coverageData >= 12X There is a 0.63% of reference with a coverageData >= 13X There is a 0.55% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.38% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 125820725 0.5047960341892187 3.3786361544854606 chr2 243199373 98509671 0.4050572572816625 19.16550386365501 chr3 198022430 77862318 0.39319948755300094 1.9623805168511452 chr4 191154276 79104229 0.41382400987985224 3.0091107341060583 chr5 180915260 73299879 0.40516139434561793 1.9437594365282298 chr6 171115067 66501708 0.38863736061301957 2.1158076625929656 chr7 159138663 112986064 0.7099850021989942 6.865986959875872 chr8 146364022 137213192 0.9374789659715692 4.120202299457586 chr9 141213431 47961108 0.3396355974099942 2.9109658006372268 chr10 135534747 58013540 0.42803444344792263 8.265577979475777 chr11 135006516 52688185 0.3902640151087226 2.066947070980881 chr12 133851895 48066503 0.35910214793746476 1.8540107181767456 chr13 115169878 36028692 0.31283086016640566 1.7183848130497954 chr14 107349540 46416655 0.43238801954810424 2.065429288771972 chr15 102531392 31067497 0.30300473244330867 1.68477494675988 chr16 90354753 32081135 0.3550575253080488 3.1152184516424684 chr17 81195210 37319589 0.4596279632751735 2.6141757442887763 chr18 78077248 22230549 0.2847250584446829 4.06508802163122 chr19 59128983 17907328 0.30285195333056886 2.4975611701093405 chr20 63025520 52115527 0.8268956289452273 2.943660877519435 chr21 48129895 15671473 0.32560787842982 2.1080207680829455 chr22 51304566 13995000 0.2727827382849316 1.5477441795442257 chrMT 16571 3767608 227.36153521211756 155.98922866471455 chrX 155270560 52387774 0.3373966964503767 1.8215357535711543 chrY 59373566 2677015 0.04508765735916889 2.0306365139073854