BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083662.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 = 1,366,196 number of mapped reads = 1,034,103 (75.69%) number of supplementary alignments = 5,893 (0.43%) number of secondary alignments = 0 number of mapped bases = 65,477,007 bp number of sequenced bases = 65,454,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,089 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5011 >>>>>>> ACTG content number of A's = 19,375,581 bp (29.6%) number of C's = 12,133,281 bp (18.54%) number of T's = 19,428,110 bp (29.68%) number of G's = 14,508,238 bp (22.17%) number of N's = 9,033 bp (0.01%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 582,454 number of insertions = 4,826 mapped reads with insertion percentage = 0.46% number of deletions = 14,305 mapped reads with deletion percentage = 1.37% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.2061X There is a 1.97% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% 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 6742175 0.027049782154805545 0.42919853561534044 chr2 243199373 6432150 0.02644805338375605 0.1967914220046242 chr3 198022430 5379921 0.02716824048669638 0.17477924028534333 chr4 191154276 3408682 0.017832099136511077 0.14077990173565752 chr5 180915260 3607202 0.019938627620467175 0.14812116712253146 chr6 171115067 4454954 0.026034843559392697 0.1902279282665734 chr7 159138663 3772340 0.023704736038909664 0.23170945950998445 chr8 146364022 4804732 0.032827274997949976 0.22917350766121125 chr9 141213431 2555987 0.018100169239567587 0.15690397521223992 chr10 135534747 3284567 0.024234132373449593 0.22131929558906238 chr11 135006516 1915688 0.014189596596952401 0.1371728969765403 chr12 133851895 2287472 0.017089575011246572 0.13746361277224614 chr13 115169878 2145138 0.018625859792957323 0.14248185808300642 chr14 107349540 1365438 0.012719551476419927 0.11927776045825428 chr15 102531392 1699344 0.016573889877550867 0.135471362519025 chr16 90354753 1946995 0.02154834068330639 0.160125479269876 chr17 81195210 1406274 0.017319667009913515 0.14374269502187761 chr18 78077248 1897678 0.024305134320308012 0.23159277156061256 chr19 59128983 1527362 0.02583102097325097 0.2967700986756612 chr20 63025520 1198044 0.019008871327043396 0.14618416744570772 chr21 48129895 729115 0.01514890069882762 0.13033660359164143 chr22 51304566 445631 0.008685991028556796 0.09728746350798381 chrMT 16571 6587 0.3975016595256774 0.6624790993228915 chrX 155270560 2349443 0.015131284385140364 0.13230934248097068 chrY 59373566 114088 0.0019215285132107443 0.051744286953321374