BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 357,494 number of mapped reads = 341,789 (95.61%) number of supplementary alignments = 10,927 (3.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,709 number of mapped paired reads (second in pair) = 170,080 number of mapped paired reads (both in pair) = 339,318 number of mapped paired reads (singletons) = 2,471 number of mapped bases = 45,786,488 bp number of sequenced bases = 44,781,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 322,776 duplication rate = 49.32% >>>>>>> Insert size mean insert size = 380,988.3327 std insert size = 5,652,359.446 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 38.1547 >>>>>>> ACTG content number of A's = 11,855,464 bp (26.47%) number of C's = 10,526,050 bp (23.51%) number of T's = 11,307,740 bp (25.25%) number of G's = 11,092,161 bp (24.77%) number of N's = 461 bp (0%) GC percentage = 48.27% >>>>>>> Mismatches and indels general error rate = 0.0405 number of mismatches = 1,772,653 number of insertions = 24,409 mapped reads with insertion percentage = 7.03% number of deletions = 139,420 mapped reads with deletion percentage = 38.82% homopolymer indels = 26.93% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 3.9698X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% 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 295586 0.0011858987504789406 0.46067001908761435 chr2 243199373 2011591 0.008271365896983624 3.0887251642426654 chr3 198022430 685123 0.003459825232929421 1.184607620275291 chr4 191154276 669884 0.0035044154596886967 1.5708932642186235 chr5 180915260 559261 0.0030912870478698147 1.4969893584164704 chr6 171115067 886659 0.0051816535828490195 2.6803691097620845 chr7 159138663 1479296 0.009295641751118645 3.195912556320856 chr8 146364022 791227 0.005405884514433472 1.957534981409768 chr9 141213431 502859 0.003560985640239844 1.5546422692308417 chr10 135534747 717391 0.005293041200718809 2.0319186646457084 chr11 135006516 1300448 0.009632483220291381 2.63929232983495 chr12 133851895 1290415 0.009640618087625879 3.07234067212089 chr13 115169878 1171913 0.010175516553034813 3.0726801177827734 chr14 107349540 212336 0.0019779870505267187 0.7694973923831687 chr15 102531392 751152 0.007326068488370859 2.676675669618657 chr16 90354753 478314 0.005293733689914464 1.9208458833538875 chr17 81195210 767665 0.00945456018895696 2.706046370886434 chr18 78077248 120106 0.0015382970465352467 0.6584301183182261 chr19 59128983 232314 0.003928936169932095 0.9329676457958622 chr20 63025520 290816 0.004614257843489431 1.4775455657097556 chr21 48129895 653776 0.013583574200608583 5.206900890123362 chr22 51304566 80614 0.0015712831485603055 0.3209559890548503 chrMT 16571 1371824 82.78462374026914 392.41256554880164 chrX 155270560 28028341 0.18051291242847323 14.243777736590255 chrY 59373566 437577 0.007369895889359248 1.9232134516599815