BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708603.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,013,205 number of mapped reads = 4,917,678 (98.09%) number of supplementary alignments = 170 (0%) number of secondary alignments = 0 number of mapped bases = 245,288,252 bp number of sequenced bases = 245,267,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,394 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7306 >>>>>>> ACTG content number of A's = 76,018,429 bp (30.99%) number of C's = 46,427,945 bp (18.93%) number of T's = 75,673,127 bp (30.85%) number of G's = 47,138,908 bp (19.22%) number of N's = 9,190 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 354,748 number of insertions = 15,714 mapped reads with insertion percentage = 0.32% number of deletions = 12,085 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.0792X std coverageData = 0.2943X There is a 7.3% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 18807715 0.07545704369579083 0.28890191411853144 chr2 243199373 22150630 0.09108012790806003 0.3140082980078153 chr3 198022430 18313511 0.09248200317509486 0.31607764376963005 chr4 191154276 19195792 0.10042041643891869 0.3290803221918895 chr5 180915260 17653983 0.09758150307497554 0.3247938772010167 chr6 171115067 16226355 0.09482715510960821 0.32031685012256594 chr7 159138663 13295803 0.08354854030663812 0.30203305479272247 chr8 146364022 13686848 0.09351237970216479 0.31841882526020765 chr9 141213431 10395018 0.07361210563604251 0.28405210433009903 chr10 135534747 9919639 0.07318889967013403 0.28110660156281003 chr11 135006516 11084513 0.08210354083946585 0.3011136610865417 chr12 133851895 11233007 0.0839211652550754 0.30261688440838924 chr13 115169878 9661859 0.08389223960105263 0.30321846751650894 chr14 107349540 7320245 0.06819074399387273 0.2737419627140812 chr15 102531392 6416797 0.06258373045398623 0.2622725081310151 chr16 90354753 4432081 0.04905199619105815 0.23076124029539657 chr17 81195210 3831268 0.04718588695072037 0.22632264733555058 chr18 78077248 7000766 0.08966461010511026 0.3107125840518264 chr19 59128983 1927096 0.03259139430827011 0.18665526390306558 chr20 63025520 3945630 0.06260368815679744 0.2612439450716348 chr21 48129895 3118176 0.06478667780181112 0.26861039724498487 chr22 51304566 1329004 0.025904205095507483 0.16773486651063083 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 14022568 0.09031053922907215 0.31298360378468976 chrY 59373566 319748 0.0053853595386202675 0.07735928230572077