BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013237.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 = 1,827,707 number of mapped reads = 1,651,121 (90.34%) number of supplementary alignments = 8,939 (0.49%) number of secondary alignments = 0 number of mapped bases = 110,938,555 bp number of sequenced bases = 110,890,622 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,608 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9804 >>>>>>> ACTG content number of A's = 31,253,052 bp (28.18%) number of C's = 20,283,341 bp (18.29%) number of T's = 35,104,361 bp (31.66%) number of G's = 24,225,344 bp (21.85%) number of N's = 24,524 bp (0.02%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 912,113 number of insertions = 8,662 mapped reads with insertion percentage = 0.52% number of deletions = 27,742 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.0358X std coverageData = 0.4366X There is a 3.17% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% 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 8149799 0.03269720639933731 0.7005311311033496 chr2 243199373 5256180 0.02161263795692434 0.47107862453428573 chr3 198022430 8127819 0.04104494122206257 0.2209872055803843 chr4 191154276 8862129 0.046361133977458086 0.2502602644150057 chr5 180915260 6251142 0.034552872985949334 0.20455256301484723 chr6 171115067 9802429 0.05728559835119604 0.36908208961035466 chr7 159138663 6296164 0.039564012172202304 0.9952092439210907 chr8 146364022 7259983 0.0496022376318683 0.49310123256296984 chr9 141213431 4412482 0.031246900303697034 0.3797397589092804 chr10 135534747 5204433 0.0383992527023347 0.39391981759029226 chr11 135006516 5948415 0.044060206694023565 0.3124056076146811 chr12 133851895 4000893 0.029890447199122584 0.1961353408945085 chr13 115169878 1515052 0.013154932750731924 0.12435289706982755 chr14 107349540 5395092 0.0502572437664847 0.2781040689627141 chr15 102531392 1914039 0.018667833944944392 0.1485943181102258 chr16 90354753 3174184 0.035130238250997155 0.24654768006386824 chr17 81195210 3174010 0.03909109909316079 0.22883707876777665 chr18 78077248 3686042 0.04721019367895754 0.8156835477699456 chr19 59128983 1789013 0.03025610976600088 0.5437318510510248 chr20 63025520 2119614 0.03363104342494913 0.20867478651024612 chr21 48129895 1830133 0.03802486998984727 0.2286967439213314 chr22 51304566 1527129 0.029765947147862043 0.1885771716890012 chrMT 16571 28309 1.708345905497556 1.72675738524269 chrX 155270560 4998552 0.03219252896363612 0.23175850548693158 chrY 59373566 215518 0.003629864509064522 0.11626577869417415