BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818751.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 = 2,028,686 number of mapped reads = 1,969,445 (97.08%) number of supplementary alignments = 18,062 (0.89%) number of secondary alignments = 0 number of mapped bases = 133,660,574 bp number of sequenced bases = 133,605,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,074,123 duplication rate = 45.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9252 >>>>>>> ACTG content number of A's = 38,088,547 bp (28.51%) number of C's = 29,164,002 bp (21.83%) number of T's = 39,789,607 bp (29.78%) number of G's = 26,554,607 bp (19.88%) number of N's = 8,446 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 697,455 number of insertions = 15,934 mapped reads with insertion percentage = 0.8% number of deletions = 34,835 mapped reads with deletion percentage = 1.75% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.5616X There is a 1.64% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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% 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 10901893 0.04373867939129428 0.7799569129652347 chr2 243199373 11767820 0.04838754251229094 0.8561736291859849 chr3 198022430 9016913 0.045534806334817726 0.4513184597445962 chr4 191154276 8962481 0.04688611307863184 0.5129167378011404 chr5 180915260 8442347 0.04666464841053209 0.4664267202049574 chr6 171115067 8036856 0.04696755312610783 0.48649698291815946 chr7 159138663 7320033 0.04599782894996422 0.5151578977926171 chr8 146364022 6975991 0.04766192473174863 0.5139488058585482 chr9 141213431 5812943 0.04116423599961961 0.4765528894787352 chr10 135534747 6517424 0.048086738967388194 0.5713078617570053 chr11 135006516 6194210 0.045880822522669944 0.48628200155097356 chr12 133851895 6163148 0.0460445330265963 0.4757058502679905 chr13 115169878 4376188 0.03799767852493514 0.40852907286239076 chr14 107349540 4165068 0.038799122939884044 0.4394797244022254 chr15 102531392 3890557 0.03794503248331984 0.4107821112863617 chr16 90354753 3848832 0.04259689581576301 0.5989545574432954 chr17 81195210 3372427 0.041534802360878184 0.4441210880373029 chr18 78077248 3588206 0.04595712697250805 0.577310536153987 chr19 59128983 2573770 0.04352806135698292 0.6497231480405866 chr20 63025520 2859814 0.04537549234024567 0.47389202348553616 chr21 48129895 1822273 0.03786156192528573 0.42808412295465254 chr22 51304566 1565593 0.03051566599354919 0.40791769945908307 chrMT 16571 138014 8.328646430511133 8.579114661064288 chrX 155270560 4074131 0.026238914833565358 0.3578387644174298 chrY 59373566 1273642 0.021451330715086238 0.879186764930441