BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524429.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 = 1,869,228 number of mapped reads = 1,571,927 (84.09%) number of supplementary alignments = 6,962 (0.37%) number of secondary alignments = 0 number of mapped bases = 91,959,691 bp number of sequenced bases = 91,933,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,212 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7539 >>>>>>> ACTG content number of A's = 22,992,154 bp (25.01%) number of C's = 17,701,111 bp (19.25%) number of T's = 29,229,607 bp (31.79%) number of G's = 22,001,823 bp (23.93%) number of N's = 9,143 bp (0.01%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 464,305 number of insertions = 6,464 mapped reads with insertion percentage = 0.41% number of deletions = 16,033 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.2909X There is a 2.62% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7792329 0.03126302742491462 0.56449192301573 chr2 243199373 7410685 0.030471645171552313 0.38668552580966326 chr3 198022430 6205914 0.03133944977849226 0.19725664964787074 chr4 191154276 6124403 0.032039058336314694 0.2511885511362819 chr5 180915260 5530821 0.030571334889052476 0.1935995080576121 chr6 171115067 3522118 0.020583330630960742 0.16849247725914032 chr7 159138663 5196840 0.03265604914627189 0.3546110569649126 chr8 146364022 4784077 0.03268615425176004 0.24389340675120816 chr9 141213431 3518502 0.024916199366333647 0.20947210754596135 chr10 135534747 4639405 0.03423037341118142 0.32995284912437906 chr11 135006516 3813764 0.028248740231175212 0.22118159278533253 chr12 133851895 4305936 0.032169406342734255 0.20401558731918698 chr13 115169878 2951747 0.025629505312144207 0.17842646996282166 chr14 107349540 2531901 0.02358557847569724 0.17504066218419415 chr15 102531392 2847411 0.027771114235921032 0.1851907211751275 chr16 90354753 2922021 0.03233942767792194 0.2150234141625699 chr17 81195210 2580707 0.03178398085305771 0.2143838335416007 chr18 78077248 2472213 0.031663680051837895 0.34423505545283256 chr19 59128983 2704558 0.04573997154661023 0.39036129810482895 chr20 63025520 2555661 0.04054962180399305 0.23472194724033216 chr21 48129895 1273682 0.026463427771866114 0.22409759631780515 chr22 51304566 683733 0.01332694247915478 0.12980418155938145 chrMT 16571 6868 0.41445899462917146 0.8345583120312726 chrX 155270560 5257204 0.033858343783908555 0.2209450590781023 chrY 59373566 327191 0.005510718355707319 0.17775634336696602