BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927008.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 8,677,748 number of mapped reads = 8,481,141 (97.73%) number of supplementary alignments = 217,304 (2.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,261,077 number of mapped paired reads (second in pair) = 4,220,064 number of mapped paired reads (both in pair) = 8,355,298 number of mapped paired reads (singletons) = 125,843 number of mapped bases = 778,477,204 bp number of sequenced bases = 777,886,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,624 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 296,206.3451 std insert size = 5,352,082.1408 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 52.6187 >>>>>>> ACTG content number of A's = 222,122,989 bp (28.55%) number of C's = 151,962,202 bp (19.54%) number of T's = 226,195,143 bp (29.08%) number of G's = 177,455,649 bp (22.81%) number of N's = 150,239 bp (0.02%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 7,307,065 number of insertions = 134,000 mapped reads with insertion percentage = 1.55% number of deletions = 400,596 mapped reads with deletion percentage = 4.6% homopolymer indels = 51.85% >>>>>>> Coverage mean coverageData = 0.2515X std coverageData = 1.0926X There is a 16.47% of reference with a coverageData >= 1X There is a 5.4% of reference with a coverageData >= 2X There is a 1.76% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 63219637 0.2536388344645288 1.3227765115829517 chr2 243199373 68973924 0.2836106160520406 1.9423656733665886 chr3 198022430 52597856 0.2656156476819318 0.6934158623344504 chr4 191154276 47979870 0.2510007675684953 0.8982976747194302 chr5 180915260 47092313 0.2603003914650428 0.6816411703990068 chr6 171115067 45582992 0.2663879505128558 0.810933151226302 chr7 159138663 39876257 0.2505755436691082 0.8511670839684298 chr8 146364022 40022367 0.2734440230127046 0.787563630377389 chr9 141213431 33348110 0.23615395337289127 1.311980317376391 chr10 135534747 38396839 0.2832988576722691 1.9063471330948152 chr11 135006516 36353368 0.26927121058364323 0.85264043543091 chr12 133851895 34541235 0.2580556293207504 0.6988154211048216 chr13 115169878 23971778 0.2081427749710736 0.6072633707330192 chr14 107349540 23241382 0.21650192446097113 0.6374201426631502 chr15 102531392 22549544 0.2199281952594577 0.6412431005030069 chr16 90354753 24523612 0.27141474228810075 1.413703462044709 chr17 81195210 20134124 0.24797182001253523 0.8121732110084444 chr18 78077248 20596538 0.2637969258342712 1.2944150670799837 chr19 59128983 12566893 0.21253355566761567 0.8774739204247032 chr20 63025520 17817580 0.282704212515819 0.7499581091181504 chr21 48129895 9985498 0.2074697648935241 0.8932964874439168 chr22 51304566 9107431 0.17751696798292768 0.5931011058974636 chrMT 16571 70996 4.284352181521936 3.8891332100071683 chrX 155270560 44389171 0.28588272625538286 0.774552055133651 chrY 59373566 1537889 0.025901913993173327 1.0190664337065451