BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867852.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 = 1,986,976 number of mapped reads = 1,836,483 (92.43%) number of supplementary alignments = 7,946 (0.4%) number of secondary alignments = 0 number of mapped bases = 108,433,567 bp number of sequenced bases = 108,399,839 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,559 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8564 >>>>>>> ACTG content number of A's = 27,393,369 bp (25.27%) number of C's = 20,210,890 bp (18.64%) number of T's = 34,812,929 bp (32.12%) number of G's = 25,967,540 bp (23.96%) number of N's = 15,111 bp (0.01%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 546,932 number of insertions = 9,201 mapped reads with insertion percentage = 0.5% number of deletions = 21,149 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 0.035X std coverageData = 0.3367X There is a 3.09% of reference with a coverageData >= 1X There is a 0.29% 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 9104410 0.03652713065858319 0.6208110906960328 chr2 243199373 9703655 0.039900000071135054 0.4544916045612519 chr3 198022430 7214915 0.03643483720505803 0.21148508584895528 chr4 191154276 6360057 0.03327185314965175 0.24160809794456356 chr5 180915260 6899802 0.03813830850974097 0.21961578359935274 chr6 171115067 6344583 0.037077874621058354 0.2510778514670368 chr7 159138663 5864942 0.03685428725764776 0.38760275415843115 chr8 146364022 5414398 0.036992683898779445 0.3701944649387757 chr9 141213431 4630546 0.03279111602351762 0.28888973389800804 chr10 135534747 5332831 0.039346596485696765 0.35644185253313565 chr11 135006516 4940807 0.03659680396463234 0.2852149579417462 chr12 133851895 4767550 0.0356180986455216 0.2119595842153836 chr13 115169878 3302329 0.02867354778304098 0.18925943157534986 chr14 107349540 3121047 0.029073687693491748 0.19783509686890158 chr15 102531392 3176150 0.03097734204174269 0.19647731868299467 chr16 90354753 3171314 0.03509847456502924 0.23115122446656874 chr17 81195210 2578770 0.031760124765980655 0.21100091002242263 chr18 78077248 2717512 0.03480542756834872 0.5235460669610084 chr19 59128983 2270749 0.038403315680230796 0.4658092277451104 chr20 63025520 2102539 0.03336012142382958 0.20869536510402872 chr21 48129895 1444823 0.030019242718065352 0.2353067740710159 chr22 51304566 1208317 0.02355184137022034 0.17091475046564614 chrMT 16571 8866 0.5350310783899583 0.8205912572073524 chrX 155270560 6379517 0.04108645579690058 0.2501988442575029 chrY 59373566 373138 0.006284581256244572 0.24340048011872578