BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068158.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 = 4,691,165 number of mapped reads = 4,431,513 (94.47%) number of supplementary alignments = 34,537 (0.74%) number of secondary alignments = 0 number of mapped bases = 284,945,401 bp number of sequenced bases = 284,825,982 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 531,314 duplication rate = 9.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9281 >>>>>>> ACTG content number of A's = 74,495,747 bp (26.15%) number of C's = 50,898,167 bp (17.87%) number of T's = 93,181,935 bp (32.72%) number of G's = 66,218,116 bp (23.25%) number of N's = 32,017 bp (0.01%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,632,818 number of insertions = 18,000 mapped reads with insertion percentage = 0.4% number of deletions = 68,063 mapped reads with deletion percentage = 1.52% homopolymer indels = 44.71% >>>>>>> Coverage mean coverageData = 0.092X std coverageData = 0.9762X There is a 6.78% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 30733237 0.12330254936456106 2.2761451145481817 chr2 243199373 24741134 0.10173189879070947 1.3413078548071111 chr3 198022430 16769204 0.08468335632483653 0.3802752028391071 chr4 191154276 12809995 0.06701390765645232 0.3725882004772491 chr5 180915260 15171223 0.08385817205248468 0.37870852614425166 chr6 171115067 20016262 0.11697545020977025 0.6173023752812171 chr7 159138663 28116672 0.17668033317585433 1.528313116011262 chr8 146364022 10466681 0.07151129667644689 0.9459714048600906 chr9 141213431 9662407 0.06842413594497254 0.6342159906557181 chr10 135534747 14970586 0.1104557047647715 0.6429004671258359 chr11 135006516 13224366 0.09795353877586176 0.5581722659953949 chr12 133851895 11318626 0.0845608200018386 0.41883712973147025 chr13 115169878 7125909 0.06187302725110119 0.35998922349460355 chr14 107349540 6045396 0.05631506199281339 0.3741590781839181 chr15 102531392 4354914 0.04247395763436041 0.3087551601631002 chr16 90354753 6105398 0.067571409331394 0.39295310055414767 chr17 81195210 8267963 0.10182821129473031 0.45902625387947527 chr18 78077248 7312226 0.09365373636119961 1.2230858873639114 chr19 59128983 6095359 0.10308580818986858 1.4042093340905077 chr20 63025520 4155516 0.06593386298121777 0.3630426506052042 chr21 48129895 5011974 0.10413432233749939 0.441781331611773 chr22 51304566 2927535 0.05706188022329241 0.30031656670973034 chrMT 16571 357287 21.560980025345483 12.48430901548806 chrX 155270560 18403621 0.1185261455874185 0.5512061544054301 chrY 59373566 781910 0.013169328586394828 0.33928928407707143