BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013349.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 = 2,018,630 number of mapped reads = 754,277 (37.37%) number of supplementary alignments = 7,955 (0.39%) number of secondary alignments = 0 number of mapped bases = 47,549,059 bp number of sequenced bases = 47,525,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,212 duplication rate = 12.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1804 >>>>>>> ACTG content number of A's = 12,779,207 bp (26.89%) number of C's = 8,981,368 bp (18.9%) number of T's = 14,834,291 bp (31.21%) number of G's = 10,925,018 bp (22.99%) number of N's = 5,146 bp (0.01%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 407,164 number of insertions = 3,510 mapped reads with insertion percentage = 0.46% number of deletions = 13,995 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.2548X There is a 0.72% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 2704102 0.010848927834767562 0.2247113206796889 chr2 243199373 4913804 0.020204838274809202 0.3277258268192335 chr3 198022430 5370646 0.0271214023583086 0.32250175992481006 chr4 191154276 1627093 0.008511936191267833 0.1757688359805883 chr5 180915260 2687246 0.014853617102283135 0.23381760882719627 chr6 171115067 4268488 0.024945132388604914 0.3334008796182575 chr7 159138663 2527460 0.01588212413221041 0.25405443227800156 chr8 146364022 3043193 0.020791947081093467 0.2891363719421056 chr9 141213431 1396243 0.009887466015891931 0.19504854592016474 chr10 135534747 2224819 0.016415118995278755 0.2630867743117821 chr11 135006516 1770036 0.01311074496582076 0.23323977858910422 chr12 133851895 1513689 0.011308685618533827 0.21192850228945304 chr13 115169878 750965 0.006520498354613174 0.15627024452907534 chr14 107349540 1642394 0.015299497324348106 0.246583377190711 chr15 102531392 697010 0.006798015577512105 0.15630916908016795 chr16 90354753 1441361 0.01595224326494479 0.24557684025962795 chr17 81195210 2192474 0.027002504211763232 0.32917974699104446 chr18 78077248 1599580 0.020487146268270112 0.3491622371107339 chr19 59128983 1202159 0.020331129321131736 0.29487662583389695 chr20 63025520 874540 0.013875966433914389 0.2415631137585762 chr21 48129895 532513 0.011064079819829235 0.202525259070835 chr22 51304566 510879 0.00995776867111594 0.19484126382103967 chrMT 16571 32981 1.9902842314887454 3.4453311494741814 chrX 155270560 1883003 0.012127237771281303 0.21119892470778207 chrY 59373566 142381 0.002398053706257091 0.09257172545299928