BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714110.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 609,844 number of mapped reads = 450,724 (73.91%) number of supplementary alignments = 14,970 (2.45%) number of secondary alignments = 0 number of mapped bases = 58,327,324 bp number of sequenced bases = 56,852,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 391,038 duplication rate = 44.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4251 >>>>>>> ACTG content number of A's = 15,793,597 bp (27.78%) number of C's = 11,753,798 bp (20.67%) number of T's = 14,912,453 bp (26.23%) number of G's = 14,391,792 bp (25.31%) number of N's = 413 bp (0%) GC percentage = 45.99% >>>>>>> Mismatches and indels general error rate = 0.0483 number of mismatches = 2,583,947 number of insertions = 62,743 mapped reads with insertion percentage = 13.27% number of deletions = 230,472 mapped reads with deletion percentage = 47.36% homopolymer indels = 30.78% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 4.2166X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 4916264 0.019724179543769323 2.9865265479652185 chr2 243199373 6863619 0.02822219035901873 10.09572828456349 chr3 198022430 4051542 0.02046001556490343 5.677328310619997 chr4 191154276 2337393 0.012227782966257057 2.0507531207853846 chr5 180915260 3185592 0.017608199551546952 3.0196378594342965 chr6 171115067 2029604 0.011861047864359016 1.6322237456413502 chr7 159138663 2244788 0.014105861879711783 2.103252103387369 chr8 146364022 3474288 0.0237373088859228 6.002799015707743 chr9 141213431 2544687 0.018020148522558028 2.8415686318023483 chr10 135534747 3449805 0.02545328837334975 4.48931652363106 chr11 135006516 2618191 0.01939307136849602 2.673586664483914 chr12 133851895 2244515 0.016768645673638016 2.560744007422739 chr13 115169878 1388718 0.012057996623040619 2.0879746644056256 chr14 107349540 1430633 0.013326866607905353 2.2623269763295184 chr15 102531392 1513909 0.014765321824558864 1.779165716215867 chr16 90354753 1386417 0.015344151292184928 2.654427874357838 chr17 81195210 1552989 0.019126608577033053 2.5859954636938447 chr18 78077248 1547905 0.01982530173194629 2.954861335865668 chr19 59128983 1306688 0.022098942577787953 2.5537958377873013 chr20 63025520 1334638 0.021176152136467893 3.2217430829215825 chr21 48129895 502025 0.010430627367876037 1.4415768771144761 chr22 51304566 487001 0.00949235200625223 1.5771445573174419 chrMT 16571 204231 12.324603222497133 95.45088004708863 chrX 155270560 5546393 0.03572082821109166 3.9068315074208377 chrY 59373566 165489 0.0027872504743946154 0.5109123951600802