BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525124.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 = 1,104,158 number of mapped reads = 1,021,914 (92.55%) number of supplementary alignments = 24,795 (2.25%) number of secondary alignments = 0 number of mapped bases = 79,915,633 bp number of sequenced bases = 79,883,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,123 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9045 >>>>>>> ACTG content number of A's = 20,546,749 bp (25.72%) number of C's = 15,477,572 bp (19.38%) number of T's = 24,858,184 bp (31.12%) number of G's = 18,998,210 bp (23.78%) number of N's = 3,228 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 590,574 number of insertions = 6,498 mapped reads with insertion percentage = 0.63% number of deletions = 18,318 mapped reads with deletion percentage = 1.77% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.2681X There is a 2.35% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6386789 0.025623964242801226 0.3871319395417417 chr2 243199373 6898529 0.028365735136989846 0.38008730438303584 chr3 198022430 5326948 0.02690073038695667 0.1749250770586387 chr4 191154276 5120278 0.02678610234175457 0.18017270838371682 chr5 180915260 4893957 0.02705110116194731 0.17776705396145798 chr6 171115067 4651077 0.027180990438439884 0.19361466497381957 chr7 159138663 4451479 0.02797232876086184 0.4074657050022514 chr8 146364022 4159688 0.028420153690501892 0.3664353099447886 chr9 141213431 3352929 0.023743697580720917 0.26210812908658393 chr10 135534747 3772258 0.027832405220780763 0.26493962896002865 chr11 135006516 3593963 0.026620663257468254 0.2585366084656019 chr12 133851895 3617108 0.027023210990027448 0.17685539236753944 chr13 115169878 2587465 0.02246650812636964 0.15910941097731485 chr14 107349540 2451911 0.02284044253939048 0.18017593945298796 chr15 102531392 2310884 0.022538307097205897 0.16029951651286417 chr16 90354753 2227273 0.02465031363651672 0.17814507458651116 chr17 81195210 2087343 0.02570771108295674 0.20034026494149218 chr18 78077248 2238958 0.028676190021451577 0.4369588158655181 chr19 59128983 1527218 0.02582858561934001 0.2880318149203203 chr20 63025520 1618210 0.025675472411810327 0.17392214332343378 chr21 48129895 1054095 0.02190104507811621 0.1669744638863495 chr22 51304566 831993 0.01621674374947446 0.13772151137952837 chrMT 16571 808 0.04875988172107899 0.21536563248491014 chrX 155270560 4578977 0.029490310333137204 0.2206613015483881 chrY 59373566 175495 0.002955776649831004 0.07775653782832245