BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082974.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 = 2,852,943 number of mapped reads = 2,251,962 (78.93%) number of supplementary alignments = 17,217 (0.6%) number of secondary alignments = 0 number of mapped bases = 148,782,165 bp number of sequenced bases = 148,724,677 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,215 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0113 >>>>>>> ACTG content number of A's = 42,837,247 bp (28.8%) number of C's = 26,709,441 bp (17.96%) number of T's = 46,926,445 bp (31.55%) number of G's = 32,237,325 bp (21.68%) number of N's = 14,219 bp (0.01%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,402,783 number of insertions = 12,326 mapped reads with insertion percentage = 0.54% number of deletions = 33,284 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.3462X There is a 4.08% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% 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 13625901 0.05466747061785655 0.5537164175662243 chr2 243199373 14817804 0.06092862747635455 0.461347872309632 chr3 198022430 11003579 0.055567336488093796 0.2689617234666293 chr4 191154276 8330576 0.043580380069551776 0.2423370552655122 chr5 180915260 8285324 0.045796711675952596 0.24613969479648704 chr6 171115067 10556917 0.06169484186918502 0.3322436299027387 chr7 159138663 7488521 0.04705657857638278 0.31206236335421145 chr8 146364022 12524903 0.08557364596061728 0.4830313457503725 chr9 141213431 5222291 0.036981546040050536 0.32717072062864533 chr10 135534747 5277410 0.03893769027362408 0.2523730938792833 chr11 135006516 5813973 0.043064388092201415 0.278948505581651 chr12 133851895 4470501 0.03339886222753888 0.21076465356410554 chr13 115169878 3468328 0.030114888200194152 0.19767200728783918 chr14 107349540 3375422 0.03144328331541989 0.2355921013512625 chr15 102531392 2933875 0.028614407185654906 0.19395029422784743 chr16 90354753 5061677 0.05602004135853263 0.2931720431404563 chr17 81195210 3540504 0.043604838265705576 0.25417569495927045 chr18 78077248 4954337 0.06345429849166814 0.6864127994636108 chr19 59128983 2524789 0.042699685871478626 0.38884298945717544 chr20 63025520 3098621 0.04916454477487849 0.2642934146385046 chr21 48129895 3642707 0.07568491474996984 0.32445357206855874 chr22 51304566 1982234 0.03863660010300058 0.22308164950894824 chrMT 16571 103804 6.264196487840203 4.946519504019183 chrX 155270560 6435928 0.04144976356110263 0.25814105256595365 chrY 59373566 242239 0.004079913273189621 0.0826816617024656