BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240181.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,868,747 number of mapped reads = 1,484,227 (79.42%) number of supplementary alignments = 14,185 (0.76%) number of secondary alignments = 0 number of mapped bases = 99,749,490 bp number of sequenced bases = 99,702,510 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,052 duplication rate = 8.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2992 >>>>>>> ACTG content number of A's = 28,584,731 bp (28.67%) number of C's = 18,756,801 bp (18.81%) number of T's = 31,282,671 bp (31.38%) number of G's = 21,002,421 bp (21.07%) number of N's = 75,886 bp (0.08%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 878,315 number of insertions = 7,151 mapped reads with insertion percentage = 0.48% number of deletions = 26,644 mapped reads with deletion percentage = 1.77% homopolymer indels = 48.5% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.4053X There is a 1.52% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 8003886 0.03211179963318928 0.6516269984735422 chr2 243199373 10554402 0.04339814642531994 0.4413359735261495 chr3 198022430 6222755 0.03142449569980532 0.3225102051093877 chr4 191154276 6471333 0.03385397980843494 0.3407415806059272 chr5 180915260 5315236 0.029379699645016126 0.31666385065579206 chr6 171115067 5115197 0.029893317343001713 0.33139030398685027 chr7 159138663 5951717 0.03739956643974067 0.5155918312459117 chr8 146364022 5738840 0.03920936253036282 0.47938460626125107 chr9 141213431 3716317 0.02631702221016073 0.36255389163932766 chr10 135534747 4715039 0.03478841481144315 0.40466723245567854 chr11 135006516 4295677 0.03181829386664567 0.38596923764405605 chr12 133851895 4775043 0.03567407842825086 0.3492627630145626 chr13 115169878 2773577 0.024082486220919675 0.28658588839528637 chr14 107349540 3209570 0.029898311627604552 0.3186132032599972 chr15 102531392 2838093 0.027680234751908957 0.3013738514464683 chr16 90354753 3010898 0.033323072666691926 0.34135947514146914 chr17 81195210 2530993 0.031171703355407296 0.33627047417238914 chr18 78077248 2402396 0.030769475891363383 0.5567708721512526 chr19 59128983 1804460 0.0305173522094909 0.4534636228818392 chr20 63025520 1949793 0.030936563474605206 0.3257764576898828 chr21 48129895 1632049 0.03390925743760712 0.3364763821032827 chr22 51304566 959068 0.018693618809678656 0.24315965012761317 chrMT 16571 12735 0.7685112546014121 1.4052786807636797 chrX 155270560 5463201 0.03518504087317003 0.362987893846426 chrY 59373566 287215 0.004837422094539513 0.11927384935885751