BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524615.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 = 1,904,116 number of mapped reads = 1,778,382 (93.4%) number of supplementary alignments = 4,320 (0.23%) number of secondary alignments = 0 number of mapped bases = 103,932,395 bp number of sequenced bases = 103,898,506 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,370 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4484 >>>>>>> ACTG content number of A's = 25,769,868 bp (24.8%) number of C's = 19,281,622 bp (18.56%) number of T's = 33,449,647 bp (32.19%) number of G's = 25,396,637 bp (24.44%) number of N's = 732 bp (0%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 489,144 number of insertions = 6,474 mapped reads with insertion percentage = 0.36% number of deletions = 19,906 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.2916X There is a 2.92% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% 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 10817051 0.04339829107186056 0.5265276796956387 chr2 243199373 8972158 0.036892192152156576 0.33014752865532077 chr3 198022430 6897436 0.03483158953255952 0.21051128195933022 chr4 191154276 4777696 0.02499392689494427 0.20582489653158878 chr5 180915260 6370679 0.03521360774099432 0.21178830319234312 chr6 171115067 6826596 0.03989476858867139 0.24009555639136165 chr7 159138663 6256421 0.03931427399261234 0.3442255834878572 chr8 146364022 9222766 0.06301252093222745 0.3954442595645189 chr9 141213431 3842141 0.02720804227184311 0.2603798805937873 chr10 135534747 4530106 0.03342394552151265 0.29719171493355084 chr11 135006516 5386227 0.039896052128328384 0.2918313663146327 chr12 133851895 3278673 0.024494782087321216 0.1800119773386216 chr13 115169878 2430189 0.021100907999572597 0.16342363116248929 chr14 107349540 1934532 0.01802086902282022 0.15485825546300272 chr15 102531392 2677999 0.02611882027311206 0.19543136066413375 chr16 90354753 3120930 0.03454085033025324 0.22140048013239966 chr17 81195210 2326696 0.028655582022634095 0.19961273986774225 chr18 78077248 2295450 0.029399729867528118 0.4103134778491261 chr19 59128983 2092839 0.03539446974760246 0.3606235187074489 chr20 63025520 1929216 0.030610076680049607 0.20084803409383234 chr21 48129895 953045 0.01980151837023538 0.17656564768568656 chr22 51304566 1893194 0.036901082059635784 0.21623703931952654 chrMT 16571 10850 0.654758312714984 0.9873715425942688 chrX 155270560 4834756 0.031137621967744562 0.22633138351516202 chrY 59373566 254749 0.004290613098765198 0.12221772405739893