BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525106.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 = 1,107,941 number of mapped reads = 990,087 (89.36%) number of supplementary alignments = 23,692 (2.14%) number of secondary alignments = 0 number of mapped bases = 76,287,165 bp number of sequenced bases = 76,257,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,001 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7229 >>>>>>> ACTG content number of A's = 20,438,583 bp (26.8%) number of C's = 14,837,081 bp (19.46%) number of T's = 23,578,164 bp (30.92%) number of G's = 17,400,746 bp (22.82%) number of N's = 2,884 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 568,265 number of insertions = 6,420 mapped reads with insertion percentage = 0.64% number of deletions = 17,584 mapped reads with deletion percentage = 1.75% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.268X There is a 2.25% 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 6015480 0.024134262839008134 0.3964896257402083 chr2 243199373 6570369 0.027016389552945105 0.3862177857107965 chr3 198022430 5109836 0.025804329337843192 0.16989685698071352 chr4 191154276 5053502 0.026436771940168368 0.1779624554273686 chr5 180915260 4711147 0.026040628081898675 0.17409198524348085 chr6 171115067 4499924 0.0262976491719458 0.19240663164470329 chr7 159138663 4274502 0.026860235717828043 0.404842967902988 chr8 146364022 4026200 0.027508126279831256 0.3441536877705243 chr9 141213431 3228972 0.02286589864104357 0.2706282933399413 chr10 135534747 3494207 0.025780894400459536 0.24715370141118456 chr11 135006516 3484074 0.025806709951688555 0.25964022960777955 chr12 133851895 3399250 0.025395606091344468 0.17117524022772748 chr13 115169878 2522697 0.021904138858252504 0.15637587985655457 chr14 107349540 2314042 0.02155614267187358 0.1779346911748336 chr15 102531392 2143470 0.020905499849255924 0.15347094345115814 chr16 90354753 2093198 0.023166440397440962 0.1738306902709134 chr17 81195210 1913397 0.023565392589045584 0.1963593350051667 chr18 78077248 2167048 0.027755179075983825 0.45410833480801854 chr19 59128983 1376024 0.023271565485914074 0.30110369568872314 chr20 63025520 1515541 0.024046465622179714 0.1690001379793465 chr21 48129895 1004370 0.02086790341013626 0.16050467478525132 chr22 51304566 754092 0.014698340884513087 0.12781178148486286 chrMT 16571 1204 0.07265705147546919 0.45618612625646593 chrX 155270560 4446454 0.02863681305715649 0.2270420888023643 chrY 59373566 168165 0.002832321036604067 0.06993402952804635