BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084342.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,434,380 number of mapped reads = 2,256,071 (92.68%) number of supplementary alignments = 10,089 (0.41%) number of secondary alignments = 0 number of mapped bases = 156,414,670 bp number of sequenced bases = 156,358,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,965 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4274 >>>>>>> ACTG content number of A's = 44,857,218 bp (28.69%) number of C's = 28,811,820 bp (18.43%) number of T's = 49,992,118 bp (31.97%) number of G's = 32,478,291 bp (20.77%) number of N's = 218,963 bp (0.14%) GC percentage = 39.2% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,459,035 number of insertions = 11,241 mapped reads with insertion percentage = 0.49% number of deletions = 32,315 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.0505X std coverageData = 0.3635X There is a 4.23% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 15338237 0.06153740736316962 0.6447610958550303 chr2 243199373 14126452 0.0580858898842638 0.3786318636577474 chr3 198022430 10710038 0.05408497411126608 0.2720041823760673 chr4 191154276 7701156 0.040287647031238785 0.24039955049474765 chr5 180915260 8090920 0.044722153344057325 0.24247648361564506 chr6 171115067 7536635 0.04404425122891136 0.26449031034564224 chr7 159138663 8807335 0.05534377902873295 0.469032094736814 chr8 146364022 7871240 0.05377851669039267 0.46383700574862435 chr9 141213431 5911305 0.041860784474530614 0.3031947433103825 chr10 135534747 10919472 0.0805658492873418 0.4919233177146966 chr11 135006516 8808750 0.0652468507520037 0.3474402597215048 chr12 133851895 8026292 0.05996397734974167 0.2835085179371182 chr13 115169878 4171361 0.03621920134360132 0.21809931260563134 chr14 107349540 4184691 0.03898191832028344 0.23377740476612546 chr15 102531392 3273699 0.03192874822181289 0.2066560860036992 chr16 90354753 3128127 0.034620503029873816 0.24005753401132168 chr17 81195210 4164307 0.05128759442829201 0.27336603901991213 chr18 78077248 4449618 0.0569899441127843 0.49986781351227333 chr19 59128983 2790642 0.04719583964432468 0.416657581311826 chr20 63025520 3084810 0.04894541131909741 0.25977993316951425 chr21 48129895 1702931 0.03538198036791894 0.23012258613894412 chr22 51304566 1073710 0.020928156764838435 0.16292622054937944 chrMT 16571 14046 0.8476253696216282 1.2065701811721086 chrX 155270560 10190672 0.0656317076463175 0.32431914226472935 chrY 59373566 338224 0.005696541791005108 0.12594801630036373