BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524499.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,159,078 number of mapped reads = 1,072,524 (92.53%) number of supplementary alignments = 2,416 (0.21%) number of secondary alignments = 0 number of mapped bases = 62,824,477 bp number of sequenced bases = 62,804,319 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,450 duplication rate = 2.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5694 >>>>>>> ACTG content number of A's = 16,213,383 bp (25.82%) number of C's = 11,738,215 bp (18.69%) number of T's = 19,029,551 bp (30.3%) number of G's = 15,821,721 bp (25.19%) number of N's = 1,449 bp (0%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 291,580 number of insertions = 4,421 mapped reads with insertion percentage = 0.41% number of deletions = 11,819 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.54% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.2036X There is a 1.84% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 6208176 0.024907364222775598 0.344089917389115 chr2 243199373 4977969 0.020468675303698253 0.22031712585702087 chr3 198022430 3432487 0.01733382930408439 0.1426792825770051 chr4 191154276 3579288 0.018724603366968365 0.16345581425407896 chr5 180915260 3466938 0.019163325415445884 0.14975250174462204 chr6 171115067 2719268 0.015891458582077987 0.16221300097404281 chr7 159138663 3148369 0.019783809544761603 0.25684651461446467 chr8 146364022 5756928 0.03933294481344603 0.2357692565468198 chr9 141213431 2687695 0.019032856725929987 0.18513339332172676 chr10 135534747 3298896 0.02433985434008299 0.21444222829652024 chr11 135006516 2178587 0.016136902606982317 0.19161824947123524 chr12 133851895 2909245 0.021734806219964237 0.15902242885244533 chr13 115169878 1407187 0.012218359734652146 0.11863659523725854 chr14 107349540 1486340 0.013845797569323538 0.1296135218123285 chr15 102531392 1673173 0.016318641221607526 0.14299625867802898 chr16 90354753 1851465 0.020491063707517413 0.16281828799431775 chr17 81195210 2179749 0.026845783144104192 0.18338975887216735 chr18 78077248 1499665 0.019207452086425998 0.29923683200612133 chr19 59128983 1269245 0.021465699824399144 0.2584410003371469 chr20 63025520 1771699 0.02811081923639821 0.18447860293127244 chr21 48129895 846864 0.01759538432402564 0.15334400561029052 chr22 51304566 493160 0.009612399800828644 0.10509527885453801 chrMT 16571 5283 0.318809969223342 0.5991346400022406 chrX 155270560 3772432 0.024295861366121177 0.1815994977538544 chrY 59373566 204369 0.0034420873423705086 0.09837030923622461