BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472820.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,650,039 number of mapped reads = 1,971,586 (74.4%) number of supplementary alignments = 19,285 (0.73%) number of secondary alignments = 0 number of mapped bases = 122,847,823 bp number of sequenced bases = 122,791,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,551 duplication rate = 4.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2406 >>>>>>> ACTG content number of A's = 32,784,093 bp (26.7%) number of C's = 24,907,526 bp (20.28%) number of T's = 35,804,470 bp (29.16%) number of G's = 29,292,777 bp (23.86%) number of N's = 2,235 bp (0%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,111,559 number of insertions = 9,342 mapped reads with insertion percentage = 0.47% number of deletions = 31,312 mapped reads with deletion percentage = 1.57% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3444X There is a 3.05% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 9670335 0.038797636536279684 0.42331201323606654 chr2 243199373 10430418 0.042888342479402694 0.4416677269966422 chr3 198022430 8116939 0.04098999795124219 0.26856266002758117 chr4 191154276 6945107 0.03633247000972136 0.27130150947005494 chr5 180915260 6685893 0.036955937271405406 0.2626828182756799 chr6 171115067 7052667 0.04121593220075705 0.2947852935016512 chr7 159138663 7287413 0.045792850477825116 0.4683182987845527 chr8 146364022 6215600 0.04246672040756027 0.3300742400555836 chr9 141213431 5583283 0.03953790344489257 0.359960445677905 chr10 135534747 5757595 0.04248058248856288 0.3328979004707481 chr11 135006516 5436660 0.040269611875622356 0.37486799992681497 chr12 133851895 5832509 0.043574347602624526 0.29772499971026894 chr13 115169878 3992704 0.03466795371616179 0.26001142088324525 chr14 107349540 3858881 0.03594687969785432 0.294063624310035 chr15 102531392 3813487 0.03719336025399909 0.29158489120503694 chr16 90354753 3996237 0.044228298648550345 0.3044383782553499 chr17 81195210 3413129 0.04203608808943286 0.3002255761889878 chr18 78077248 2849034 0.03648993878472766 0.55384981916831 chr19 59128983 2916808 0.049329581738282224 0.38050878708208313 chr20 63025520 3386000 0.05372426915319382 0.3308873256905868 chr21 48129895 1801543 0.037430852487835266 0.2816873600083074 chr22 51304566 1607821 0.03133875062894012 0.24810874982394593 chrMT 16571 157066 9.478365819805685 7.040018954636123 chrX 155270560 5427869 0.034957489687678076 0.28609846618243173 chrY 59373566 612825 0.010321512438717257 0.15781408703669497