BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173889.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,487,094 number of mapped reads = 6,329,460 (97.57%) number of supplementary alignments = 658,991 (10.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,168,996 number of mapped paired reads (second in pair) = 3,160,464 number of mapped paired reads (both in pair) = 6,225,812 number of mapped paired reads (singletons) = 103,648 number of mapped bases = 751,678,424 bp number of sequenced bases = 751,211,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,157,360 duplication rate = 66.79% >>>>>>> Insert size mean insert size = 1,001,464.5137 std insert size = 9,024,482.1076 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 52.7009 >>>>>>> ACTG content number of A's = 222,213,706 bp (29.58%) number of C's = 150,548,566 bp (20.04%) number of T's = 221,985,551 bp (29.55%) number of G's = 156,455,530 bp (20.83%) number of N's = 8,377 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 7,796,642 number of insertions = 75,009 mapped reads with insertion percentage = 1.15% number of deletions = 193,197 mapped reads with deletion percentage = 2.98% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.2428X std coverageData = 3.2644X There is a 4.45% of reference with a coverageData >= 1X There is a 3.61% of reference with a coverageData >= 2X There is a 2.91% of reference with a coverageData >= 3X There is a 2.47% of reference with a coverageData >= 4X There is a 1.98% of reference with a coverageData >= 5X There is a 1.65% of reference with a coverageData >= 6X There is a 1.28% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.68% of reference with a coverageData >= 10X There is a 0.52% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 66299716 0.2659961918409824 2.4929881251450188 chr2 243199373 54327814 0.22338796901421287 9.786068258645752 chr3 198022430 53296620 0.2691443590506389 1.6250406797871428 chr4 191154276 32499854 0.17001897462131582 1.3789251163439435 chr5 180915260 40547821 0.22412604110897003 1.446113417849573 chr6 171115067 41791103 0.24422807256359255 1.838076040951457 chr7 159138663 41078217 0.25812845367439086 2.0993206804931686 chr8 146364022 42320428 0.2891450195321908 1.844669431678394 chr9 141213431 33637255 0.23820152772861952 1.922136223265978 chr10 135534747 33801936 0.2493968281063748 2.31285840238162 chr11 135006516 30694504 0.22735572259341913 1.51072729467825 chr12 133851895 34471150 0.25753202821670923 1.5597243157392506 chr13 115169878 18286884 0.15878183008928776 1.233687329818055 chr14 107349540 25176736 0.23453045071269052 1.4872899593842375 chr15 102531392 24277938 0.2367854129981967 1.483941958418537 chr16 90354753 26667802 0.2951455359520489 1.8171753896355651 chr17 81195210 38528577 0.47451785641049515 2.469983683619147 chr18 78077248 14386853 0.18426434548512777 2.6683028672201297 chr19 59128983 15194576 0.25697340338155317 1.9575361364990806 chr20 63025520 42117723 0.6682645855202781 2.8974105356402724 chr21 48129895 8587253 0.1784182782862917 1.3079542102747816 chr22 51304566 8407634 0.16387691497088192 1.1723214969877391 chrMT 16571 813577 49.096433528453325 42.41752245174607 chrX 155270560 23464486 0.15111999338445098 1.1831609019999394 chrY 59373566 1001967 0.016875641257592645 0.5806617515040227