BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240248.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 = 1,945,352 number of mapped reads = 1,263,183 (64.93%) number of supplementary alignments = 12,099 (0.62%) number of secondary alignments = 0 number of mapped bases = 80,884,330 bp number of sequenced bases = 80,848,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,121 duplication rate = 13.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9132 >>>>>>> ACTG content number of A's = 22,350,570 bp (27.64%) number of C's = 14,383,885 bp (17.79%) number of T's = 26,349,499 bp (32.59%) number of G's = 17,757,850 bp (21.96%) number of N's = 7,027 bp (0.01%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 673,717 number of insertions = 5,573 mapped reads with insertion percentage = 0.44% number of deletions = 21,100 mapped reads with deletion percentage = 1.65% homopolymer indels = 48.38% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.419X There is a 1.02% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 5758672 0.02310394243711834 0.5924151202391867 chr2 243199373 6918187 0.02844656593748702 0.4422485994823329 chr3 198022430 5007332 0.02528669100768029 0.35255364732535605 chr4 191154276 5154876 0.026967097508192806 0.35870941477774015 chr5 180915260 4876835 0.02695646016814723 0.36223074828843044 chr6 171115067 4444649 0.025974620925695573 0.3652933750214817 chr7 159138663 4242466 0.026658927001290692 0.4287532210218946 chr8 146364022 4392469 0.03001057869262434 0.616321749702533 chr9 141213431 3336075 0.023624346327227187 0.38385179158919364 chr10 135534747 3855773 0.028448594071599956 0.39325072647112413 chr11 135006516 3452616 0.02557369897612942 0.3837497967542051 chr12 133851895 4376046 0.032693194220373194 0.415428225993792 chr13 115169878 2552812 0.022165622160336056 0.3381584866676306 chr14 107349540 3107711 0.028949458004198247 0.3969182681581304 chr15 102531392 2768511 0.02700159381431201 0.37886805548019276 chr16 90354753 2430142 0.0268955635349919 0.3601160689707475 chr17 81195210 1959935 0.024138554478767896 0.3366792199182951 chr18 78077248 2166822 0.02775228450674901 0.5504155871634868 chr19 59128983 1361089 0.0230189820785519 0.41906935386816696 chr20 63025520 1859444 0.02950303305708545 0.40032302504345624 chr21 48129895 1054272 0.02190472262613496 0.31388897162012575 chr22 51304566 812692 0.015840539417095935 0.25517540989975673 chrMT 16571 32722 1.9746545169271619 3.1972356963513713 chrX 155270560 4751039 0.03059845343508776 0.393474328899786 chrY 59373566 211143 0.0035561785189051976 0.11452144917830889