BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716790.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 = 999,326 number of mapped reads = 897,165 (89.78%) number of supplementary alignments = 2,389 (0.24%) number of secondary alignments = 0 number of mapped bases = 51,156,530 bp number of sequenced bases = 51,139,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,036 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7186 >>>>>>> ACTG content number of A's = 12,320,246 bp (24.09%) number of C's = 9,757,946 bp (19.08%) number of T's = 17,173,116 bp (33.58%) number of G's = 11,887,515 bp (23.25%) number of N's = 485 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 261,695 number of insertions = 3,411 mapped reads with insertion percentage = 0.38% number of deletions = 10,737 mapped reads with deletion percentage = 1.19% homopolymer indels = 43.17% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.1674X There is a 1.53% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4148623 0.016644383806770937 0.20584643192506097 chr2 243199373 4329338 0.01780160017106623 0.23628188602072475 chr3 198022430 3381064 0.017074146600463393 0.13975990579480574 chr4 191154276 3309154 0.01731143068962789 0.14969570419905662 chr5 180915260 3109591 0.017188107846734434 0.1390332771998134 chr6 171115067 2956844 0.017279857652745447 0.1562668261198307 chr7 159138663 2918604 0.01834000578476646 0.22461702866268257 chr8 146364022 2535336 0.017322125788535654 0.16222236641339344 chr9 141213431 2103568 0.014896373419324399 0.14405140244957693 chr10 135534747 2461741 0.01816317257743507 0.17946829102377254 chr11 135006516 2090308 0.015483015649407619 0.15263482935656136 chr12 133851895 2294341 0.017140892924975025 0.1392351427571204 chr13 115169878 1639718 0.01423738592481621 0.127127784300298 chr14 107349540 1538486 0.014331556520875637 0.12932325884769696 chr15 102531392 1468063 0.014318180718740267 0.12800877654071827 chr16 90354753 1543582 0.017083572792235956 0.14871903114186852 chr17 81195210 1409881 0.01736409081274622 0.14557093758261677 chr18 78077248 1380087 0.017675917573324304 0.22171999741649673 chr19 59128983 1099036 0.018587094589467234 0.18178178125560143 chr20 63025520 1100044 0.017453945639797974 0.14230951662699184 chr21 48129895 683192 0.014194753593374762 0.1340991836783343 chr22 51304566 604045 0.011773708406382387 0.11547774927166603 chrMT 16571 16683 1.0067587954860902 1.1849210156037848 chrX 155270560 2880372 0.01855066407952673 0.15488158208199188 chrY 59373566 154829 0.00260770929608641 0.07793433674361588