BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238664.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 = 2,508,477 number of mapped reads = 2,350,195 (93.69%) number of supplementary alignments = 15,815 (0.63%) number of secondary alignments = 0 number of mapped bases = 147,252,004 bp number of sequenced bases = 147,185,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 365,289 duplication rate = 13.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.109 >>>>>>> ACTG content number of A's = 35,600,815 bp (24.19%) number of C's = 26,381,518 bp (17.92%) number of T's = 49,067,953 bp (33.34%) number of G's = 36,127,863 bp (24.55%) number of N's = 7,471 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 782,130 number of insertions = 9,460 mapped reads with insertion percentage = 0.4% number of deletions = 39,401 mapped reads with deletion percentage = 1.66% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.5875X There is a 3.3% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.1% 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% 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 10883621 0.043665371650167324 0.4666948334265983 chr2 243199373 15124460 0.062189551779806604 1.5638726202713993 chr3 198022430 8417835 0.042509502585136444 0.2955770247185065 chr4 191154276 8280748 0.043319711038009946 0.29492414457623445 chr5 180915260 7912751 0.043737333158076326 0.2938801345428328 chr6 171115067 13184393 0.07704986609975147 0.628372032400627 chr7 159138663 8766624 0.05508795810355652 0.5577404702083767 chr8 146364022 9888646 0.06756199962856992 0.44650294228437426 chr9 141213431 5734417 0.0406081557497176 0.3118242813367375 chr10 135534747 9193167 0.0678288572007295 0.3819761147935859 chr11 135006516 5694932 0.042182645465793665 0.2934404691586417 chr12 133851895 4096465 0.03060446025063747 0.24586569212493511 chr13 115169878 3460978 0.030051069429803512 0.37088048905054355 chr14 107349540 3371106 0.03140307820601746 0.2523519851039867 chr15 102531392 3477976 0.033921084383600295 0.36364865154023757 chr16 90354753 4730176 0.05235115854945672 0.3382146951919873 chr17 81195210 4184527 0.05153662389690229 0.3167911715372934 chr18 78077248 4853998 0.06216917379055163 1.0027656579371018 chr19 59128983 3140577 0.053114003330650895 0.3955146354547664 chr20 63025520 2959334 0.04695453524223204 0.30023983211786137 chr21 48129895 1586157 0.03295575442248524 0.2629575438510967 chr22 51304566 1894111 0.03691895571244088 0.2669862345507917 chrMT 16571 17043 1.0284834952628086 1.4106010351763092 chrX 155270560 6130479 0.0394825587026929 0.27823550484858917 chrY 59373566 267483 0.0045050856470369325 0.2089763544327275