BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708505.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 = 2,953,672 number of mapped reads = 1,961,451 (66.41%) number of supplementary alignments = 378 (0.01%) number of secondary alignments = 0 number of mapped bases = 93,167,435 bp number of sequenced bases = 93,146,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,164 duplication rate = 4.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5411 >>>>>>> ACTG content number of A's = 26,573,857 bp (28.53%) number of C's = 17,026,449 bp (18.28%) number of T's = 30,104,014 bp (32.32%) number of G's = 19,440,964 bp (20.87%) number of N's = 1,308 bp (0%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 474,997 number of insertions = 4,730 mapped reads with insertion percentage = 0.24% number of deletions = 13,938 mapped reads with deletion percentage = 0.71% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.3312X There is a 2.45% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 7411767 0.029736202743502894 0.5206166642774218 chr2 243199373 8139708 0.03346928036693581 0.4822246141617609 chr3 198022430 6575253 0.033204586975323955 0.22521957527955583 chr4 191154276 6518070 0.034098478655010575 0.2359312245261597 chr5 180915260 6018676 0.033267928863491114 0.22257164655540956 chr6 171115067 5602967 0.032743855337998964 0.280803968482315 chr7 159138663 5340350 0.033557841314778424 0.37822391899620295 chr8 146364022 4921202 0.03362303066528194 0.6325625812302866 chr9 141213431 4011078 0.02840436615409479 0.24756568428486314 chr10 135534747 4383339 0.03234107191715199 0.25144705553866653 chr11 135006516 4262241 0.0315706317463966 0.28775145167638666 chr12 133851895 4287510 0.032031746730219995 0.2203980361030416 chr13 115169878 3176117 0.0275776709601099 0.22851424369651815 chr14 107349540 2912809 0.027133875003097357 0.20436891228961268 chr15 102531392 2612656 0.02548152277109434 0.1952944557580418 chr16 90354753 2395251 0.026509407867010604 0.20198084052472737 chr17 81195210 2272280 0.027985394704933948 0.24805417015712872 chr18 78077248 2534985 0.032467653060722634 0.36997032381037476 chr19 59128983 1626307 0.027504396617137827 0.3621258580613436 chr20 63025520 1835200 0.029118363481967304 0.20857807912036244 chr21 48129895 1259053 0.02615947946697162 0.2133244625928376 chr22 51304566 898018 0.017503666242883725 0.1654786048734651 chrMT 16571 91411 5.516323698026673 3.7297389792648143 chrX 155270560 3325499 0.021417447067879448 0.1982541696367147 chrY 59373566 755688 0.0127276842357759 0.1540771465107417