BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708509.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 = 3,084,965 number of mapped reads = 2,078,990 (67.39%) number of supplementary alignments = 370 (0.01%) number of secondary alignments = 0 number of mapped bases = 98,717,301 bp number of sequenced bases = 98,694,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,555 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5654 >>>>>>> ACTG content number of A's = 28,007,413 bp (28.38%) number of C's = 18,188,844 bp (18.43%) number of T's = 31,745,036 bp (32.16%) number of G's = 20,751,848 bp (21.03%) number of N's = 1,349 bp (0%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 498,893 number of insertions = 5,199 mapped reads with insertion percentage = 0.25% number of deletions = 15,172 mapped reads with deletion percentage = 0.73% homopolymer indels = 48.42% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.3262X There is a 2.61% of reference with a coverageData >= 1X There is a 0.42% 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 8076332 0.032402454876932885 0.4348746589456092 chr2 243199373 8643466 0.03554065906247217 0.5028858658817089 chr3 198022430 6897320 0.03483100374033386 0.23160306900687885 chr4 191154276 6525975 0.034139832686766576 0.2370723008022733 chr5 180915260 6205356 0.034299793173887046 0.22409362373483532 chr6 171115067 6026941 0.03522156818604407 0.2938895763430808 chr7 159138663 5445436 0.03421818367293936 0.3707045209467889 chr8 146364022 5149882 0.03518543648657045 0.643262842786073 chr9 141213431 4281899 0.030322179481638685 0.24910477924738778 chr10 135534747 4557994 0.0336297082548138 0.24958020118222715 chr11 135006516 4586086 0.033969367819254 0.28850450700680563 chr12 133851895 4607431 0.034421858577347746 0.22638672824638087 chr13 115169878 3238071 0.02811560675613462 0.23134731954558768 chr14 107349540 3201794 0.029825875360062093 0.21537462053706 chr15 102531392 2908837 0.028370208803953426 0.20691602730119762 chr16 90354753 2640848 0.029227549324383633 0.20968249502286712 chr17 81195210 2757201 0.03395768050849305 0.2635638549879783 chr18 78077248 2577430 0.03301128134024396 0.3578490694995964 chr19 59128983 1870808 0.031639441523964654 0.3386749127224561 chr20 63025520 1977305 0.031373085061416395 0.2154838189529487 chr21 48129895 1283503 0.02666747974413823 0.20659471695390136 chr22 51304566 1127127 0.021969331150759563 0.17924743605208113 chrMT 16571 135142 8.155331603403535 5.807760987542962 chrX 155270560 3261298 0.021003968814178296 0.19843616158796953 chrY 59373566 733819 0.012359355340051496 0.1510076178957208