BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716477.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 = 913,531 number of mapped reads = 827,553 (90.59%) number of supplementary alignments = 4,717 (0.52%) number of secondary alignments = 0 number of mapped bases = 47,695,240 bp number of sequenced bases = 47,682,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,787 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7148 >>>>>>> ACTG content number of A's = 12,008,469 bp (25.18%) number of C's = 9,876,794 bp (20.71%) number of T's = 14,978,816 bp (31.41%) number of G's = 10,817,852 bp (22.69%) number of N's = 276 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 231,626 number of insertions = 3,743 mapped reads with insertion percentage = 0.45% number of deletions = 8,333 mapped reads with deletion percentage = 1% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1598X There is a 1.41% of reference with a coverageData >= 1X There is a 0.1% 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 5628066 0.0225799477546738 0.2346473783067402 chr2 243199373 4912186 0.020198185297130678 0.21205519450556126 chr3 198022430 3017377 0.01523755162483361 0.13191378592436184 chr4 191154276 2022483 0.010580370171787316 0.11880126059167063 chr5 180915260 3401218 0.01880006142102109 0.14684110729741867 chr6 171115067 1778955 0.010396249910593788 0.1147545588740334 chr7 159138663 3185853 0.0200193525567071 0.21905498011075938 chr8 146364022 2101143 0.014355597579847867 0.15089094825354954 chr9 141213431 1296418 0.009180557336645974 0.12026732251061434 chr10 135534747 2127916 0.015700151046875086 0.1497337481690043 chr11 135006516 2037179 0.015089486495599961 0.15138144831138853 chr12 133851895 1877616 0.014027563823433356 0.12723261127503535 chr13 115169878 1381042 0.011991347251405441 0.11782841071047455 chr14 107349540 1032975 0.00962253773979842 0.108075745911241 chr15 102531392 2076383 0.020251192922456373 0.1521793998723693 chr16 90354753 1387957 0.01536119522124088 0.1363224374271665 chr17 81195210 1790612 0.022053172841107253 0.1660309925606263 chr18 78077248 1510154 0.01934179339927555 0.2391639940973806 chr19 59128983 761476 0.012878219129863946 0.1702421977708652 chr20 63025520 1274478 0.02022161816356295 0.153057100638785 chr21 48129895 612093 0.012717522030746171 0.12429651363685346 chr22 51304566 543127 0.010586328710002146 0.10945978339095463 chrMT 16571 24930 1.5044354595377467 1.5287650743885879 chrX 155270560 1803200 0.011613276850421612 0.12196678582896911 chrY 59373566 110403 0.0018594638563565475 0.058174168963855806