BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819123.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,841,610 number of mapped reads = 1,685,771 (91.54%) number of supplementary alignments = 6,060 (0.33%) number of secondary alignments = 0 number of mapped bases = 97,730,374 bp number of sequenced bases = 97,699,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,879 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7262 >>>>>>> ACTG content number of A's = 23,154,218 bp (23.7%) number of C's = 18,271,226 bp (18.7%) number of T's = 31,404,648 bp (32.14%) number of G's = 24,867,974 bp (25.45%) number of N's = 1,552 bp (0%) GC percentage = 44.15% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 488,354 number of insertions = 5,772 mapped reads with insertion percentage = 0.34% number of deletions = 18,480 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3011X There is a 2.78% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9655437 0.03873786537125619 0.5809578432554781 chr2 243199373 7640247 0.03141557030247771 0.3483964044280531 chr3 198022430 5313722 0.026833939973365643 0.1833686435674542 chr4 191154276 5500881 0.028777179956989297 0.21510928491381542 chr5 180915260 5348934 0.029565963645078918 0.1922332225943593 chr6 171115067 4194811 0.024514562472748237 0.22154781176901125 chr7 159138663 4889249 0.030723200181718254 0.3717553949126755 chr8 146364022 8817333 0.060242489100224374 0.32710866735558 chr9 141213431 4198433 0.029731116723592674 0.24452142849594638 chr10 135534747 5132005 0.03786486575283901 0.31078941518770686 chr11 135006516 3328808 0.024656646942877926 0.2697990545757279 chr12 133851895 4531092 0.03385153419008375 0.2052102097716968 chr13 115169878 2164002 0.018789652620800727 0.15224545797122127 chr14 107349540 2313432 0.021550460300062767 0.16763050934705442 chr15 102531392 2547137 0.02484250872162157 0.17908658104548963 chr16 90354753 3097840 0.03428530206927797 0.22357556269695827 chr17 81195210 3475140 0.042799815407830094 0.24365523246978069 chr18 78077248 2298457 0.029438243007745356 0.4440154074136789 chr19 59128983 2072182 0.035045114846639594 0.3979233370582424 chr20 63025520 2755199 0.04371560916911118 0.2338987163190222 chr21 48129895 1353627 0.02812445362700251 0.20588013930135682 chr22 51304566 836161 0.01629798408196261 0.14100267883318832 chrMT 16571 131009 7.905919980689156 5.235189963146156 chrX 155270560 5806218 0.037394197586458115 0.23829425874392998 chrY 59373566 329018 0.005541489625197853 0.164725130277479