BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971304.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,681,204 number of mapped reads = 7,319,210 (84.31%) number of secondary alignments = 0 number of mapped bases = 288,741,705 bp number of sequenced bases = 288,710,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,112 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9869 >>>>>>> ACTG content number of A's = 84,195,002 bp (29.16%) number of C's = 58,485,696 bp (20.26%) number of T's = 86,118,996 bp (29.83%) number of G's = 59,894,464 bp (20.75%) number of N's = 16,683 bp (0.01%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 841,511 number of insertions = 9,647 mapped reads with insertion percentage = 0.13% number of deletions = 24,452 mapped reads with deletion percentage = 0.33% homopolymer indels = 40.81% >>>>>>> Coverage mean coverageData = 0.0933X std coverageData = 0.7574X There is a 7.55% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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% 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 23227796 0.09319052408699917 1.2387016046855428 chr2 243199373 24394774 0.1003077174874131 0.6280764848384386 chr3 198022430 20337572 0.10270337557215109 0.3824488100498487 chr4 191154276 19725158 0.10318972932627465 0.44115555162334885 chr5 180915260 17932432 0.09912061591708737 0.38320924805570483 chr6 171115067 17534846 0.10247400364808319 0.4150437895623994 chr7 159138663 16488839 0.10361302960048119 1.0513088397816888 chr8 146364022 15401271 0.10522579790817718 1.867324587421252 chr9 141213431 12312912 0.08719363245270911 0.5921242135432793 chr10 135534747 13689359 0.1010025790655735 0.715947911125897 chr11 135006516 13268217 0.09827834532075475 0.5690877946605772 chr12 133851895 13147478 0.09822407071636902 0.3868920975960599 chr13 115169878 9785687 0.08496741656702979 0.3391144939379748 chr14 107349540 8899294 0.08290015960944033 0.43013753836502927 chr15 102531392 8234362 0.08031064281269097 0.33162407839871194 chr16 90354753 7716171 0.08539861760233022 0.4110754737995712 chr17 81195210 7118115 0.08766668624910262 0.3910612817895975 chr18 78077248 8979363 0.11500614109759606 1.1207284581732457 chr19 59128983 5207245 0.08806586441711672 1.1397175916684286 chr20 63025520 5768626 0.09152841579093675 0.3839288383529499 chr21 48129895 3784269 0.07862616363488846 0.4395405457169121 chr22 51304566 3000399 0.05848210469220225 0.3083889459318326 chrMT 16571 15301 0.9233600868987991 1.1985941302735168 chrX 155270560 10220689 0.06582502826034761 0.39230871445271004 chrY 59373566 2551530 0.042974174736279104 0.43879531554497997