BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716966.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 = 986,330 number of mapped reads = 822,764 (83.42%) number of supplementary alignments = 3,169 (0.32%) number of secondary alignments = 0 number of mapped bases = 44,785,656 bp number of sequenced bases = 44,773,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,401 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9774 >>>>>>> ACTG content number of A's = 10,834,309 bp (24.2%) number of C's = 10,177,102 bp (22.73%) number of T's = 12,648,724 bp (28.25%) number of G's = 11,112,455 bp (24.82%) number of N's = 1,178 bp (0%) GC percentage = 47.55% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 233,431 number of insertions = 3,156 mapped reads with insertion percentage = 0.38% number of deletions = 7,104 mapped reads with deletion percentage = 0.86% homopolymer indels = 34.04% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1432X There is a 1.33% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4372019 0.017540654392191064 0.17207442106303952 chr2 243199373 3846820 0.015817557227008148 0.16474640511053854 chr3 198022430 2875490 0.014521031784126677 0.13017277258733786 chr4 191154276 2835787 0.014835069658603922 0.14422137872601118 chr5 180915260 2801036 0.01548258560388991 0.13241639412919942 chr6 171115067 1903822 0.01112597524798912 0.11488953390313421 chr7 159138663 2507327 0.01575561182137115 0.1534149399084436 chr8 146364022 2749205 0.018783338708743602 0.15222302277624025 chr9 141213431 1866445 0.013217191783974146 0.12874300943549996 chr10 135534747 2286315 0.01686884766162584 0.19372416325796327 chr11 135006516 1795849 0.0133019431447294 0.1408686841089507 chr12 133851895 2131729 0.015926027793629668 0.13543414781833252 chr13 115169878 757312 0.006575608250622615 0.08772545863661929 chr14 107349540 1930584 0.01798409196723153 0.14553541297957018 chr15 102531392 855770 0.008346419406848587 0.09998524828091274 chr16 90354753 1227111 0.01358103430375157 0.13255102851433273 chr17 81195210 1809074 0.02228055078618554 0.1644025705808459 chr18 78077248 1175810 0.015059572796418234 0.16273999948295048 chr19 59128983 1184935 0.0200398339338933 0.17233355506105838 chr20 63025520 1108787 0.017592667224324367 0.14626464466532557 chr21 48129895 620669 0.012895706504242321 0.13134370263783804 chr22 51304566 508717 0.009915628172354094 0.10753523659315907 chrMT 16571 37293 2.2504978577032166 2.4360406586533503 chrX 155270560 1450779 0.009343554888962853 0.10892497240228727 chrY 59373566 146971 0.002475360836504245 0.08193679734454956