BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716297.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 = 3,825,377 number of mapped reads = 3,452,608 (90.26%) number of supplementary alignments = 15,952 (0.42%) number of secondary alignments = 0 number of mapped bases = 197,267,812 bp number of sequenced bases = 197,216,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,335 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7525 >>>>>>> ACTG content number of A's = 48,244,926 bp (24.46%) number of C's = 39,916,666 bp (20.24%) number of T's = 59,855,327 bp (30.35%) number of G's = 49,195,443 bp (24.94%) number of N's = 4,201 bp (0%) GC percentage = 45.18% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 950,483 number of insertions = 10,128 mapped reads with insertion percentage = 0.29% number of deletions = 29,920 mapped reads with deletion percentage = 0.86% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.0637X std coverageData = 0.4159X There is a 5.27% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 22692541 0.09104306705017197 0.6423617611981448 chr2 243199373 17059924 0.07014789466583041 0.5167318850647961 chr3 198022430 13461109 0.06797769828397722 0.31080939008005587 chr4 191154276 12656228 0.06620949457599369 0.3510353951581273 chr5 180915260 10315014 0.05701572106189384 0.28908978356846465 chr6 171115067 10612377 0.062018951259271635 0.32879468015339103 chr7 159138663 10215754 0.06419404189665713 0.4000508337828934 chr8 146364022 12676875 0.08661196123730462 0.42301231599655265 chr9 141213431 7402408 0.05241999962453996 0.44764137275381416 chr10 135534747 9650904 0.07120612399121533 0.46454232964601927 chr11 135006516 7659424 0.05673373572576305 0.41787088314888615 chr12 133851895 9126467 0.06818332306763382 0.3133917682858815 chr13 115169878 3433993 0.029816763372797876 0.2025125170055925 chr14 107349540 4303239 0.04008623604721548 0.2795313843580698 chr15 102531392 5824099 0.0568030813431266 0.28316774551304963 chr16 90354753 6070705 0.0671874450257199 0.3537307912166686 chr17 81195210 4560943 0.05617256239623002 0.29655098877444164 chr18 78077248 4931891 0.0631668139737712 0.8139003015669739 chr19 59128983 3425435 0.05793157308320355 0.46903602049581583 chr20 63025520 4432604 0.07033030429578367 0.3306019398762715 chr21 48129895 2576122 0.05352436359979593 0.32305802438001446 chr22 51304566 2517287 0.04906555490597075 0.26068786902367197 chrMT 16571 36113 2.179289119546195 1.9633724039778597 chrX 155270560 11049269 0.07116139080067722 0.3793572872050464 chrY 59373566 577087 0.009719594743559785 0.20224439786992435