BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927030.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 37,709,452 number of mapped reads = 37,038,309 (98.22%) number of supplementary alignments = 259,876 (0.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,623,839 number of mapped paired reads (second in pair) = 18,414,470 number of mapped paired reads (both in pair) = 36,641,640 number of mapped paired reads (singletons) = 396,669 number of mapped bases = 3,493,249,165 bp number of sequenced bases = 3,490,710,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,935,983 duplication rate = 6.22% >>>>>>> Insert size mean insert size = 78,822.8507 std insert size = 2,772,072.8016 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.6555 >>>>>>> ACTG content number of A's = 1,000,760,484 bp (28.67%) number of C's = 696,993,474 bp (19.97%) number of T's = 1,013,005,559 bp (29.02%) number of G's = 779,414,311 bp (22.33%) number of N's = 536,612 bp (0.02%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 36,364,250 number of insertions = 546,802 mapped reads with insertion percentage = 1.45% number of deletions = 1,809,490 mapped reads with deletion percentage = 4.76% homopolymer indels = 53.05% >>>>>>> Coverage mean coverageData = 1.1284X std coverageData = 4.2366X There is a 38.17% of reference with a coverageData >= 1X There is a 23.39% of reference with a coverageData >= 2X There is a 14.91% of reference with a coverageData >= 3X There is a 9.97% of reference with a coverageData >= 4X There is a 6.83% of reference with a coverageData >= 5X There is a 4.79% of reference with a coverageData >= 6X There is a 3.41% of reference with a coverageData >= 7X There is a 2.46% of reference with a coverageData >= 8X There is a 1.8% of reference with a coverageData >= 9X There is a 1.33% of reference with a coverageData >= 10X There is a 0.98% of reference with a coverageData >= 11X There is a 0.74% of reference with a coverageData >= 12X There is a 0.56% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 285142609 1.1439995930842635 5.999621868478991 chr2 243199373 306213164 1.2591034270470756 6.803147106963546 chr3 198022430 233986717 1.1816172390168125 2.2673339059056357 chr4 191154276 207797593 1.0870674585380449 3.314548472015571 chr5 180915260 217165236 1.2003699190438661 2.261180405199813 chr6 171115067 205550280 1.2012400988628313 2.3588555414783245 chr7 159138663 181345704 1.1395452279249072 2.8726823176391134 chr8 146364022 181860655 1.2425229405078797 2.72469710763688 chr9 141213431 148431448 1.0511142385599286 5.1484426640769785 chr10 135534747 170458173 1.257671385183609 8.966922261599306 chr11 135006516 165574065 1.226415360574152 3.344132718675593 chr12 133851895 158440944 1.1837034059174134 2.2853213961889645 chr13 115169878 109755659 0.9529892790196409 2.016751335965274 chr14 107349540 106504141 0.992124800907391 2.191300192025344 chr15 102531392 105163488 1.0256711232399927 2.2304292043242704 chr16 90354753 110732782 1.2255335588156608 6.013639470131308 chr17 81195210 89481556 1.1020546162760094 3.5364022499092855 chr18 78077248 94947696 1.2160738042406414 5.213957417204458 chr19 59128983 52010837 0.8796166340286962 3.2330627656599815 chr20 63025520 78754924 1.2495719829047027 2.524493712843201 chr21 48129895 44931214 0.9335406611628801 2.7339264879122953 chr22 51304566 42656244 0.8314317287081232 2.093417618943535 chrMT 16571 191161 11.53587592782572 8.269786759920636 chrX 155270560 191249405 1.2317171072223865 2.702011445585695 chrY 59373566 4903470 0.08258675249520973 2.4320607508381196