BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818924.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 651,161 number of mapped reads = 623,239 (95.71%) number of supplementary alignments = 8,709 (1.34%) number of secondary alignments = 0 number of mapped bases = 57,680,249 bp number of sequenced bases = 57,647,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,590 duplication rate = 14.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1735 >>>>>>> ACTG content number of A's = 16,936,430 bp (29.38%) number of C's = 11,953,582 bp (20.74%) number of T's = 16,583,210 bp (28.77%) number of G's = 12,171,661 bp (21.11%) number of N's = 2,593 bp (0%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 394,857 number of insertions = 7,912 mapped reads with insertion percentage = 1.23% number of deletions = 17,824 mapped reads with deletion percentage = 2.8% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.2474X There is a 1.43% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.07% 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 6983818 0.02801926018069981 0.45734948618721116 chr2 243199373 5086552 0.02091515260608834 0.3275769999545428 chr3 198022430 3852207 0.019453387174372117 0.1735720051201669 chr4 191154276 3617326 0.01892359446879441 0.19170630210826461 chr5 180915260 3052098 0.016870318181009165 0.16327133410757844 chr6 171115067 2744055 0.016036314324091635 0.16472268923499375 chr7 159138663 3014814 0.018944572884843202 0.2181859856853776 chr8 146364022 3532358 0.02413405939336649 0.21969771579016625 chr9 141213431 2107968 0.014927531928602458 0.25104395271285224 chr10 135534747 2930340 0.02162058117834536 0.2988077136001291 chr11 135006516 2188842 0.016212861903643228 0.18204628874720272 chr12 133851895 2598262 0.019411469669517938 0.1760587717176332 chr13 115169878 918599 0.00797603519211855 0.10940067564973179 chr14 107349540 1621552 0.015105346515690706 0.1597850119826236 chr15 102531392 1517056 0.014796014863428363 0.15136715531080083 chr16 90354753 1793021 0.01984423553235766 0.24774407076907776 chr17 81195210 1264898 0.015578480553224753 0.1667993606082367 chr18 78077248 1513462 0.01938416169586305 0.30832880217153974 chr19 59128983 928096 0.015696126551001225 0.3935415830063846 chr20 63025520 1259712 0.019987332115625544 0.18164679372364875 chr21 48129895 790068 0.016415327729262654 0.17214484585694115 chr22 51304566 713570 0.013908508650087791 0.15268606221165387 chrMT 16571 6360 0.3838030293886911 0.8235495286546896 chrX 155270560 3451803 0.022230891677082892 0.20692477583579102 chrY 59373566 193412 0.0032575439379874875 0.1914783162364613