BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084904.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,896,618 number of mapped reads = 1,700,352 (89.65%) number of supplementary alignments = 12,888 (0.68%) number of secondary alignments = 0 number of mapped bases = 115,351,017 bp number of sequenced bases = 115,307,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,322 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1913 >>>>>>> ACTG content number of A's = 32,850,762 bp (28.49%) number of C's = 20,916,548 bp (18.14%) number of T's = 37,086,487 bp (32.16%) number of G's = 24,436,757 bp (21.19%) number of N's = 17,209 bp (0.01%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 943,839 number of insertions = 8,648 mapped reads with insertion percentage = 0.51% number of deletions = 24,828 mapped reads with deletion percentage = 1.45% homopolymer indels = 48.87% >>>>>>> Coverage mean coverageData = 0.0373X std coverageData = 0.2854X There is a 3.2% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 8917913 0.0357788998246869 0.4334763318124628 chr2 243199373 9509177 0.039100335180551636 0.32351835300112175 chr3 198022430 9987503 0.050436220785695846 0.25427089273577425 chr4 191154276 6962045 0.036421079066000075 0.21710450002145396 chr5 180915260 5696440 0.03148678558127158 0.2023554742874959 chr6 171115067 7085529 0.041407978410223804 0.23944559507554689 chr7 159138663 6627950 0.04164889835727726 0.28113787172383 chr8 146364022 6734170 0.04600973591720512 0.4642283641227273 chr9 141213431 8562737 0.060636845513653725 0.34170650945848796 chr10 135534747 3678777 0.027142685410406233 0.2156924805937052 chr11 135006516 4304064 0.03188041679410496 0.23333472860064292 chr12 133851895 4952179 0.03699745154896761 0.2193714992445881 chr13 115169878 3466101 0.030095551546907084 0.1948977699020475 chr14 107349540 2321538 0.02162597063760124 0.17313034210232012 chr15 102531392 2996258 0.029222835480474118 0.19210968518940147 chr16 90354753 2249395 0.02489514857065682 0.18596343780594582 chr17 81195210 3174416 0.03909609938812893 0.22503293115378398 chr18 78077248 4545390 0.05821657546126626 0.49594164232561666 chr19 59128983 2245702 0.03797971630934359 0.31045837070683896 chr20 63025520 2202770 0.03495044547034281 0.21415990746682692 chr21 48129895 1053980 0.021898655710759395 0.17400929924274666 chr22 51304566 1001532 0.019521303425507976 0.15547485580390846 chrMT 16571 49912 3.0120089312654637 2.202058197919682 chrX 155270560 6762944 0.04355586789923344 0.24774746901771194 chrY 59373566 262595 0.004422759448202926 0.12036670007595195