BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013173.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 = 2,259,086 number of mapped reads = 2,065,004 (91.41%) number of supplementary alignments = 14,074 (0.62%) number of secondary alignments = 0 number of mapped bases = 135,174,364 bp number of sequenced bases = 135,124,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,383 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.642 >>>>>>> ACTG content number of A's = 37,014,357 bp (27.39%) number of C's = 26,369,800 bp (19.52%) number of T's = 40,466,851 bp (29.95%) number of G's = 31,240,994 bp (23.12%) number of N's = 32,927 bp (0.02%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,013,602 number of insertions = 9,468 mapped reads with insertion percentage = 0.45% number of deletions = 28,400 mapped reads with deletion percentage = 1.36% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0437X std coverageData = 0.3254X There is a 3.86% of reference with a coverageData >= 1X There is a 0.37% 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 10063286 0.04037416620919873 0.38018292196164943 chr2 243199373 13516398 0.05557743769347629 0.44244132761964805 chr3 198022430 8494490 0.04289660519770412 0.22713546167551216 chr4 191154276 8236843 0.04309002744986987 0.23216564901820047 chr5 180915260 7273604 0.04020448026330117 0.22135365075801405 chr6 171115067 7221196 0.042200819171581194 0.2709195080975084 chr7 159138663 8320218 0.05228281954335635 0.5870066197124307 chr8 146364022 7264258 0.04963144562944574 0.3195913459028556 chr9 141213431 4877609 0.03454068756391876 0.2676609203579479 chr10 135534747 6331209 0.046712810848423984 0.31928827689845374 chr11 135006516 5716309 0.04234098597137341 0.2725830401329996 chr12 133851895 6654823 0.04971780937430882 0.25020816221158443 chr13 115169878 3387935 0.029416849777335007 0.19128308433173488 chr14 107349540 4467470 0.041616107530595844 0.24213049054210214 chr15 102531392 3865644 0.037702053240435865 0.2307738717803909 chr16 90354753 4597463 0.050882359226857715 0.2825297380230832 chr17 81195210 3739204 0.046052026960703714 0.24753584422612995 chr18 78077248 3237296 0.04146273188317293 0.4717677459690051 chr19 59128983 2971756 0.05025887220147182 0.3443126223025964 chr20 63025520 3168403 0.050271747063729104 0.25125506795484226 chr21 48129895 2248150 0.046710054115015213 0.253957776397486 chr22 51304566 1473118 0.028713194845074803 0.18639783370091687 chrMT 16571 408361 24.64311145977913 21.62019692401224 chrX 155270560 7311425 0.047088288984080434 0.25481918190212854 chrY 59373566 327896 0.005522592326692994 0.10135014102044093