BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708606.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 = 5,182,410 number of mapped reads = 5,085,868 (98.14%) number of supplementary alignments = 151 (0%) number of secondary alignments = 0 number of mapped bases = 253,676,246 bp number of sequenced bases = 253,654,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,961 duplication rate = 1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8554 >>>>>>> ACTG content number of A's = 78,756,455 bp (31.05%) number of C's = 47,969,495 bp (18.91%) number of T's = 78,177,968 bp (30.82%) number of G's = 48,740,966 bp (19.22%) number of N's = 9,250 bp (0%) GC percentage = 38.13% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 373,813 number of insertions = 15,843 mapped reads with insertion percentage = 0.31% number of deletions = 12,903 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.0819X std coverageData = 0.3003X There is a 7.52% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.05% 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 21256770 0.08528271630665266 0.3092435504601857 chr2 243199373 21883676 0.08998245238074688 0.3131767383985933 chr3 198022430 19315610 0.09754253596423396 0.32558144850848836 chr4 191154276 20126485 0.10528922198946782 0.33916205122278253 chr5 180915260 16751419 0.09259262596201116 0.3167246795205133 chr6 171115067 16122000 0.09421730232557488 0.3201332911328112 chr7 159138663 14844149 0.09327808038703957 0.3206030679975036 chr8 146364022 13281108 0.09074025036016023 0.314011410483733 chr9 141213431 9039312 0.06401170154983346 0.264609356307088 chr10 135534747 11496231 0.08482128202888076 0.30386114816470716 chr11 135006516 10909520 0.08080735895740025 0.29822068455847267 chr12 133851895 11694937 0.08737221837613879 0.30935621927272433 chr13 115169878 9513652 0.08260538402237433 0.30150096320009645 chr14 107349540 7610881 0.07089812401618116 0.280266225342072 chr15 102531392 7657848 0.07468783804281132 0.28912057225905613 chr16 90354753 4460389 0.049365294596068456 0.23172635966942023 chr17 81195210 4574993 0.056345602160521535 0.2483299180033191 chr18 78077248 6769671 0.08670478498422485 0.30590778199950336 chr19 59128983 2255879 0.03815183156456454 0.2028191030858993 chr20 63025520 3696574 0.058652019055138296 0.25374261200301046 chr21 48129895 3193240 0.06634629059548125 0.27318720631498816 chr22 51304566 1458059 0.028419673211932055 0.17572853964571356 chrMT 16571 300 0.018103916480598635 0.1543074966277671 chrX 155270560 15422157 0.09932441153042793 0.3299680014125538 chrY 59373566 341386 0.005749797814064259 0.08004211473119435