BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174081.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 = 2,587,848 number of mapped reads = 2,530,957 (97.8%) number of supplementary alignments = 301,582 (11.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,266,903 number of mapped paired reads (second in pair) = 1,264,054 number of mapped paired reads (both in pair) = 2,499,978 number of mapped paired reads (singletons) = 30,979 number of mapped bases = 281,075,765 bp number of sequenced bases = 280,859,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,964,033 duplication rate = 61.73% >>>>>>> Insert size mean insert size = 654,534.4039 std insert size = 7,872,498.1609 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 52.6321 >>>>>>> ACTG content number of A's = 84,507,051 bp (30.09%) number of C's = 55,409,539 bp (19.73%) number of T's = 83,533,730 bp (29.74%) number of G's = 57,406,517 bp (20.44%) number of N's = 2,305 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,515,681 number of insertions = 40,008 mapped reads with insertion percentage = 1.5% number of deletions = 84,943 mapped reads with deletion percentage = 3.26% homopolymer indels = 40.07% >>>>>>> Coverage mean coverageData = 0.0908X std coverageData = 1.9412X There is a 2.04% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.62% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 21785440 0.08740375415152928 1.0162293067179826 chr2 243199373 26440927 0.1087211972376261 5.720375209147955 chr3 198022430 18782116 0.09484842701910082 0.9261593948504979 chr4 191154276 21099051 0.11037708097097446 1.9479092947539982 chr5 180915260 17457997 0.09649820031765148 0.937178191332466 chr6 171115067 16364882 0.09563670977027405 0.9904089504353991 chr7 159138663 15040437 0.0945115204342266 1.065858975518333 chr8 146364022 14708440 0.10049218242991437 1.3831742313279585 chr9 141213431 11672460 0.08265828481994747 0.9483815985372743 chr10 135534747 14103946 0.10406147731253004 1.5579144424351488 chr11 135006516 12655607 0.09374071248531442 0.9362706852415532 chr12 133851895 12493012 0.09333459193835096 0.930547743435102 chr13 115169878 9048379 0.07856549956578056 0.8538706273614668 chr14 107349540 8847867 0.0824210984043341 0.8664627065457766 chr15 102531392 7769015 0.07577206208221576 0.8139732878695561 chr16 90354753 8402068 0.09298977332160932 1.007678291124702 chr17 81195210 7546336 0.09294065499676643 0.949742190170692 chr18 78077248 7403797 0.094826562022268 1.2172616309418902 chr19 59128983 4911522 0.08306454382954634 0.9009067274176765 chr20 63025520 5973588 0.09478046353286732 1.0972235061756623 chr21 48129895 3974077 0.08256982484586763 1.4476461192093166 chr22 51304566 3208227 0.06253297221147919 0.8063788108900287 chrMT 16571 907327 54.753907428640396 45.345087293063465 chrX 155270560 7608518 0.049001678103047994 0.6649263639002889 chrY 59373566 2870729 0.04835028773579138 1.6042960738928673