BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080675.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,548,396 number of mapped reads = 1,405,582 (90.78%) number of supplementary alignments = 12,421 (0.8%) number of secondary alignments = 0 number of mapped bases = 92,194,189 bp number of sequenced bases = 92,159,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,143 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4923 >>>>>>> ACTG content number of A's = 24,692,733 bp (26.79%) number of C's = 17,157,285 bp (18.62%) number of T's = 28,933,337 bp (31.39%) number of G's = 21,371,908 bp (23.19%) number of N's = 4,256 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 642,720 number of insertions = 6,729 mapped reads with insertion percentage = 0.47% number of deletions = 21,538 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.2363X There is a 2.61% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 8256848 0.03312668978265053 0.2334989127884228 chr2 243199373 4919902 0.020229912352611207 0.3714914823566236 chr3 198022430 4390240 0.022170417765300626 0.16448248061377474 chr4 191154276 5230300 0.027361668854323718 0.1866215190500484 chr5 180915260 3885741 0.021478237933052192 0.16161134800116506 chr6 171115067 6750714 0.039451312607089124 0.2543849664476322 chr7 159138663 5570646 0.0350049817874868 0.36433501363971416 chr8 146364022 13442766 0.09184474310223588 0.3764908988914453 chr9 141213431 3339509 0.023648664127422836 0.19960325037171917 chr10 135534747 5773561 0.0425983825387596 0.23308105055291642 chr11 135006516 4041177 0.02993319966867377 0.20255022785488783 chr12 133851895 1497218 0.011185631701366648 0.12015351585342414 chr13 115169878 3319669 0.028824107984207467 0.1886214684877098 chr14 107349540 1760239 0.01639726635065227 0.14672645062233278 chr15 102531392 1672810 0.01631510084248149 0.15263102795740782 chr16 90354753 948524 0.010497776470043584 0.12076508107464441 chr17 81195210 1592183 0.019609321781420358 0.15814239568212984 chr18 78077248 2133055 0.027319802562713276 0.24152317562255854 chr19 59128983 1444030 0.02442169519472371 0.18807629197609582 chr20 63025520 3679321 0.05837827280123988 0.2744195030392978 chr21 48129895 1351965 0.02808992207441965 0.18938293814478535 chr22 51304566 1799179 0.03506859408965666 0.21058232811584546 chrMT 16571 10906 0.658137710458029 0.9352441823564096 chrX 155270560 5198246 0.0334786323949627 0.20968591362927289 chrY 59373566 185440 0.003123275432033171 0.0675646968606552