BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716338.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 = 1,679,452 number of mapped reads = 1,507,246 (89.75%) number of supplementary alignments = 6,464 (0.38%) number of secondary alignments = 0 number of mapped bases = 86,217,327 bp number of sequenced bases = 86,191,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,071 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.184 >>>>>>> ACTG content number of A's = 21,024,162 bp (24.39%) number of C's = 17,429,032 bp (20.22%) number of T's = 27,412,284 bp (31.8%) number of G's = 20,324,634 bp (23.58%) number of N's = 1,331 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 474,220 number of insertions = 6,073 mapped reads with insertion percentage = 0.4% number of deletions = 15,471 mapped reads with deletion percentage = 1.02% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0279X std coverageData = 0.2681X There is a 2.53% of reference with a coverageData >= 1X There is a 0.18% 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 6905436 0.027704789549952615 0.4940319652692793 chr2 243199373 7393580 0.0304013119310139 0.29206685021731155 chr3 198022430 5771003 0.029143178376308178 0.18452854637668412 chr4 191154276 5616511 0.029382084029341827 0.20572853877974606 chr5 180915260 5223019 0.028869974815833668 0.18380913214039807 chr6 171115067 4927453 0.028796137513711753 0.20115695739719067 chr7 159138663 4806821 0.03020523680031169 0.30446290284218547 chr8 146364022 4321757 0.02952745449971305 0.2761592368718329 chr9 141213431 3621622 0.025646441520141238 0.2598297097350607 chr10 135534747 4062392 0.029973066611471963 0.2818025121736723 chr11 135006516 3919960 0.029035339301697112 0.2451230955898914 chr12 133851895 3928990 0.02935326391905023 0.19033571320750164 chr13 115169878 2662856 0.023121115054059536 0.16235985815441 chr14 107349540 2654401 0.024726710519672464 0.1850115901798706 chr15 102531392 2464010 0.024031761901759804 0.16693214420144664 chr16 90354753 2526373 0.027960598818747254 0.19994354460861916 chr17 81195210 2275405 0.02802388219699167 0.1957115700567386 chr18 78077248 2293994 0.02938108166927195 0.4530206600033116 chr19 59128983 1783077 0.030155719065893625 0.36909075337128455 chr20 63025520 1817878 0.028843522433452354 0.1883419848665428 chr21 48129895 1153152 0.02395916301084804 0.1915806591929381 chr22 51304566 972045 0.018946559259462405 0.1464937456702574 chrMT 16571 10772 0.6500512944300284 0.8618762862045786 chrX 155270560 4838807 0.031163711910358282 0.2198342901107929 chrY 59373566 266013 0.004480327154343399 0.11530631101867302