BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708557.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 = 4,177,906 number of mapped reads = 3,440,023 (82.34%) number of supplementary alignments = 93 (0%) number of secondary alignments = 0 number of mapped bases = 171,540,607 bp number of sequenced bases = 171,524,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,798 duplication rate = 0.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1114 >>>>>>> ACTG content number of A's = 53,208,776 bp (31.02%) number of C's = 32,499,813 bp (18.95%) number of T's = 52,989,781 bp (30.89%) number of G's = 32,819,117 bp (19.13%) number of N's = 7,142 bp (0%) GC percentage = 38.08% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 271,000 number of insertions = 11,409 mapped reads with insertion percentage = 0.33% number of deletions = 9,330 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.0554X std coverageData = 0.2446X There is a 5.19% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.02% 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 15318136 0.06145676162628297 0.2588107346663872 chr2 243199373 10144261 0.04171170704457367 0.21094353992760653 chr3 198022430 14483686 0.07314164360067696 0.28035658393955104 chr4 191154276 16213027 0.08481644951536423 0.3016138531998493 chr5 180915260 9203012 0.05086918593821218 0.23372092647744674 chr6 171115067 9242093 0.05401098314738117 0.2395387105016153 chr7 159138663 10404603 0.06538073654671837 0.2652330602615654 chr8 146364022 10231437 0.06990404376835176 0.2731605543550962 chr9 141213431 8234570 0.05831293766950539 0.25158884343647436 chr10 135534747 7205752 0.05316534807122191 0.2386264626715637 chr11 135006516 8898488 0.06591154459537346 0.2671891903015744 chr12 133851895 8662934 0.0647202940234802 0.263296999747398 chr13 115169878 6504643 0.05647868273334456 0.2467064324501711 chr14 107349540 5231808 0.04873619393245653 0.2302098117193683 chr15 102531392 5329831 0.05198243090272294 0.23766233226445152 chr16 90354753 3952708 0.04374654203304612 0.21738321796406787 chr17 81195210 3434154 0.04229503193599721 0.2134008741596165 chr18 78077248 3080198 0.03945064764577768 0.20456143131223667 chr19 59128983 1339038 0.02264605159875657 0.15423239715820056 chr20 63025520 2552825 0.04050462415859481 0.2087689593736294 chr21 48129895 1897477 0.03942408351399894 0.20673890899075978 chr22 51304566 1043881 0.020346746525445707 0.14707423966171676 chrMT 16571 250 0.01508659706716553 0.14073874908542003 chrX 155270560 8642116 0.05565843260950434 0.24503716007022922 chrY 59373566 289679 0.004878922044197244 0.0728523635677149