BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080755.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 = 8,442,008 number of mapped reads = 6,238,976 (73.9%) number of supplementary alignments = 40,311 (0.48%) number of secondary alignments = 0 number of mapped bases = 392,839,155 bp number of sequenced bases = 392,710,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 550,513 duplication rate = 7.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6405 >>>>>>> ACTG content number of A's = 121,551,960 bp (30.95%) number of C's = 80,267,277 bp (20.44%) number of T's = 99,424,020 bp (25.32%) number of G's = 90,589,424 bp (23.07%) number of N's = 877,570 bp (0.22%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 4,048,697 number of insertions = 29,396 mapped reads with insertion percentage = 0.47% number of deletions = 68,034 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.1269X std coverageData = 0.733X There is a 8.13% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.21% 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 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 48339763 0.19394039142634673 0.9968996752300582 chr2 243199373 28066936 0.1154071067444734 0.7439871147864718 chr3 198022430 24988934 0.12619244193700682 0.5310738564075188 chr4 191154276 21842914 0.11426850843765587 0.6761737960679367 chr5 180915260 30122939 0.1665030302032012 0.6108581264862132 chr6 171115067 26938124 0.1574269552779943 0.8202550193249815 chr7 159138663 26278615 0.16513029897706255 1.1799348066970585 chr8 146364022 16005945 0.10935710006657237 0.8478812925778416 chr9 141213431 13742561 0.09731766236881532 0.5465885636118019 chr10 135534747 16452699 0.12139100388773368 0.9511123217277484 chr11 135006516 15437107 0.1143434217649169 0.6266513750862102 chr12 133851895 13605990 0.10164958815114272 0.5043763770714554 chr13 115169878 15904264 0.1380939554351182 0.5567340351676653 chr14 107349540 10855991 0.10112750366699289 0.5556023428553633 chr15 102531392 10844622 0.10576879713093137 0.4906948180319004 chr16 90354753 12234942 0.13541005418940164 0.6580582054744394 chr17 81195210 8481045 0.10445252866517618 0.4922276761387787 chr18 78077248 4397669 0.05632459023145898 0.7574139602571723 chr19 59128983 7789348 0.1317348549695164 0.8814997402404378 chr20 63025520 7726752 0.12259719554872375 0.5554218557321883 chr21 48129895 6298163 0.13085760939224986 0.6883845474901688 chr22 51304566 2671270 0.052066905701921344 0.3298867988370635 chrMT 16571 33995 2.0514754691931687 2.5331897960111003 chrX 155270560 22522390 0.14505254569829593 0.6114590669635149 chrY 59373566 1256177 0.021157176242370217 0.6334827188488892