BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054606.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,125,263 number of mapped reads = 5,670,088 (79.58%) number of supplementary alignments = 165 (0%) number of secondary alignments = 0 number of mapped bases = 268,700,018 bp number of sequenced bases = 268,644,127 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 850,273 duplication rate = 11.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8851 >>>>>>> ACTG content number of A's = 80,810,537 bp (30.08%) number of C's = 50,053,762 bp (18.63%) number of T's = 82,171,918 bp (30.59%) number of G's = 55,605,412 bp (20.7%) number of N's = 2,498 bp (0%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,358,646 number of insertions = 11,444 mapped reads with insertion percentage = 0.2% number of deletions = 37,744 mapped reads with deletion percentage = 0.66% homopolymer indels = 48.98% >>>>>>> Coverage mean coverageData = 0.0868X std coverageData = 0.6173X There is a 4.87% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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% 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 24165800 0.09695382062859534 0.7003216184287435 chr2 243199373 19932185 0.08195820883140188 0.632699944924411 chr3 198022430 20487596 0.10346098671751477 0.6416494008212384 chr4 191154276 16599736 0.08683946991591232 0.5971180650307247 chr5 180915260 13871946 0.07667648378583432 0.5222790681838021 chr6 171115067 14021754 0.08194342114829666 0.5961520556376193 chr7 159138663 17566248 0.11038328253392451 0.7464449818937577 chr8 146364022 15017053 0.10260071289923968 0.6868918259864242 chr9 141213431 12338121 0.08737214946643425 0.612615827851393 chr10 135534747 11645822 0.08592499161856997 0.6094819405630316 chr11 135006516 12315425 0.09122096743834202 0.6168957824849004 chr12 133851895 10112689 0.07555133231397285 0.5154574683477234 chr13 115169878 7802953 0.0677516824321026 0.48909999647715613 chr14 107349540 6196972 0.05772704754952839 0.5042103246273809 chr15 102531392 7200359 0.07022589725495973 0.5022808979147183 chr16 90354753 7328672 0.08110997768982889 0.5897187209279406 chr17 81195210 4686717 0.05772159466057172 0.4307092823591692 chr18 78077248 10453315 0.133884265490505 0.8284594981215223 chr19 59128983 4366765 0.07385151542349376 0.6009867413771791 chr20 63025520 4826006 0.07657225200204615 0.5458084693005846 chr21 48129895 3527328 0.07328767286942969 0.6001103012832926 chr22 51304566 3092311 0.06027360215852912 0.45560119198795823 chrMT 16571 24861 1.500271558747209 3.3967503448461747 chrX 155270560 20460787 0.131775057679962 0.7959051665787371 chrY 59373566 658597 0.011092427899648136 0.2384831614104525