BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080725.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 = 1,360,324 number of mapped reads = 1,184,220 (87.05%) number of supplementary alignments = 18,957 (1.39%) number of secondary alignments = 0 number of mapped bases = 80,677,806 bp number of sequenced bases = 80,649,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,025 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2077 >>>>>>> ACTG content number of A's = 23,700,089 bp (29.39%) number of C's = 15,326,817 bp (19%) number of T's = 23,754,118 bp (29.45%) number of G's = 17,867,289 bp (22.15%) number of N's = 1,185 bp (0%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 730,395 number of insertions = 7,434 mapped reads with insertion percentage = 0.62% number of deletions = 16,141 mapped reads with deletion percentage = 1.35% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.5019X There is a 2.32% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 9484634 0.03805259927516891 0.8592920741281452 chr2 243199373 5495674 0.022597402008927053 0.38870076761693784 chr3 198022430 4816575 0.024323380942249825 0.16686918114121174 chr4 191154276 3474651 0.018177207817208337 0.1543474509953687 chr5 180915260 3636417 0.020100112063515262 0.1561766243583778 chr6 171115067 4737158 0.027684049587521128 0.3258912943545869 chr7 159138663 5505326 0.03459452213696178 1.4642204583130627 chr8 146364022 9218320 0.06298214461474692 0.6811098824319556 chr9 141213431 2609552 0.018479488682631044 0.3355561047279252 chr10 135534747 3837056 0.02831049664334416 0.34243214000770256 chr11 135006516 3410566 0.025262232528095164 0.2966536715384546 chr12 133851895 2594099 0.019380368130014147 0.15595107759961482 chr13 115169878 1627376 0.014130222487515356 0.12429725665947833 chr14 107349540 1572210 0.014645707843741109 0.17621329949114886 chr15 102531392 1434126 0.013987189406342986 0.12780858967765585 chr16 90354753 2017874 0.022332793051849747 0.19673931790466279 chr17 81195210 1365247 0.016814378582184836 0.17507850579492665 chr18 78077248 2521248 0.032291711920993935 0.5884598680233353 chr19 59128983 1514322 0.025610486146869803 0.4928489571774398 chr20 63025520 1976651 0.031362708312442325 0.20273046297349362 chr21 48129895 1162020 0.02414341439971976 0.18067665656916052 chr22 51304566 774968 0.015105244238885093 0.12909333459884917 chrMT 16571 44093 2.6608532979301187 2.260009502839002 chrX 155270560 5623401 0.036216788295218356 0.25315847691907534 chrY 59373566 224242 0.003776798584070224 0.10377650383177904