BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013325.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 = 2,859,009 number of mapped reads = 2,438,245 (85.28%) number of supplementary alignments = 11,825 (0.41%) number of secondary alignments = 0 number of mapped bases = 156,676,579 bp number of sequenced bases = 156,597,305 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,130 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8072 >>>>>>> ACTG content number of A's = 41,287,667 bp (26.37%) number of C's = 28,671,262 bp (18.31%) number of T's = 49,409,052 bp (31.55%) number of G's = 37,227,157 bp (23.77%) number of N's = 2,167 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,212,602 number of insertions = 10,266 mapped reads with insertion percentage = 0.42% number of deletions = 45,581 mapped reads with deletion percentage = 1.85% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.472X There is a 4.02% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9656215 0.03874098672757168 0.7883460565053481 chr2 243199373 19551614 0.08039335693517598 0.5802611540768797 chr3 198022430 8701942 0.04394422389423259 0.2521215847733021 chr4 191154276 9228855 0.04827961578008331 0.2818443408904279 chr5 180915260 6040411 0.03338806798276718 0.22759171486701718 chr6 171115067 6463474 0.03777267609052802 0.3081070040257017 chr7 159138663 10646663 0.06690179997302101 0.9770446602458998 chr8 146364022 10904755 0.0745043409643389 0.4744343179764231 chr9 141213431 5244015 0.03713538409813157 0.3952597744829725 chr10 135534747 8132249 0.060001211349883586 0.4524232219096127 chr11 135006516 6397189 0.04738429810306341 0.4100756287828159 chr12 133851895 9115816 0.06810375004403188 0.32086752339175817 chr13 115169878 2405324 0.02088500953348236 0.17473039162961432 chr14 107349540 5596477 0.05213321826996185 0.29576464627271437 chr15 102531392 3869837 0.03774294803293025 0.2721065758572809 chr16 90354753 6419501 0.07104774001208326 0.34037453240778803 chr17 81195210 4724561 0.05818768126839009 0.3701343366958106 chr18 78077248 4096969 0.05247327620973526 0.7040143353476583 chr19 59128983 2701395 0.04568647832146885 0.5268621048806305 chr20 63025520 3869423 0.061394543035900376 0.3160483286488714 chr21 48129895 3321095 0.0690027476685748 0.3311771300788917 chr22 51304566 1647175 0.032105816858483904 0.21378227528007868 chrMT 16571 23957 1.4457184237523384 1.8137454471967527 chrX 155270560 7604099 0.048973218103934194 0.3153584015534027 chrY 59373566 313568 0.0052812728142352106 0.11165352454560681