BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549123.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,815,948 number of mapped reads = 6,889,973 (58.31%) number of secondary alignments = 0 number of mapped bases = 273,526,835 bp number of sequenced bases = 273,501,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 332,326 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8816 >>>>>>> ACTG content number of A's = 80,650,676 bp (29.49%) number of C's = 55,708,031 bp (20.37%) number of T's = 81,268,455 bp (29.71%) number of G's = 55,862,670 bp (20.43%) number of N's = 11,472 bp (0%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 827,014 number of insertions = 6,675 mapped reads with insertion percentage = 0.1% number of deletions = 20,366 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.0884X std coverageData = 0.691X There is a 6.53% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 22186433 0.08901254853844476 1.110631793514796 chr2 243199373 23450228 0.0964238834612456 0.5326592534633635 chr3 198022430 18805222 0.09496511077053241 0.39348132359142024 chr4 191154276 18342888 0.0959585544400796 0.44003629060690386 chr5 180915260 17310389 0.09568230452201766 0.4065977214597303 chr6 171115067 16052227 0.09380954746667633 0.4049171956269916 chr7 159138663 14990153 0.09419554442279059 0.7399159831397301 chr8 146364022 14656740 0.10013895354693109 1.8584290768008764 chr9 141213431 12067035 0.08545245954685429 0.4839788376936781 chr10 135534747 13900677 0.10256172168159948 0.5904246274446683 chr11 135006516 12514965 0.0926989701741507 0.4951709009657409 chr12 133851895 12256643 0.09156869239692124 0.40399805228689556 chr13 115169878 8931958 0.07755463629127053 0.357885771970644 chr14 107349540 8446064 0.07867815735400449 0.43898100713685145 chr15 102531392 8028684 0.07830464254303697 0.35370788124246383 chr16 90354753 7607650 0.08419756291071927 0.3975166827867534 chr17 81195210 6872785 0.08464520259261599 0.3950634873711538 chr18 78077248 7272511 0.0931450734534086 0.9333900522982864 chr19 59128983 5053243 0.08546135488242712 0.8592746582792545 chr20 63025520 5789442 0.0918586947001786 0.4199821831625367 chr21 48129895 3684104 0.07654502466710139 0.42711697953917044 chr22 51304566 2953725 0.05757236110329829 0.3148839054045064 chrMT 16571 142426 8.59489469555247 10.726930807875878 chrX 155270560 9767318 0.06290515085409623 0.3788213100381413 chrY 59373566 2443325 0.0411517307213786 0.4178609657434912