BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124869.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,147,290 number of mapped reads = 6,083,844 (98.97%) number of supplementary alignments = 28,357 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,043,920 number of mapped paired reads (second in pair) = 3,039,924 number of mapped paired reads (both in pair) = 6,062,546 number of mapped paired reads (singletons) = 21,298 number of mapped bases = 557,195,466 bp number of sequenced bases = 556,891,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 365,718 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 63,620.6973 std insert size = 2,404,176.3172 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.7814 >>>>>>> ACTG content number of A's = 160,264,009 bp (28.78%) number of C's = 109,646,614 bp (19.69%) number of T's = 165,663,595 bp (29.75%) number of G's = 121,307,852 bp (21.78%) number of N's = 9,341 bp (0%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 4,188,016 number of insertions = 89,918 mapped reads with insertion percentage = 1.44% number of deletions = 178,990 mapped reads with deletion percentage = 2.88% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.18X std coverageData = 2.0063X There is a 11.56% of reference with a coverageData >= 1X There is a 3.82% of reference with a coverageData >= 2X There is a 1.14% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 45560902 0.18279152853143743 2.5805625408629433 chr2 243199373 51755450 0.2128107871396527 2.06782722697098 chr3 198022430 39544564 0.19969739791598357 0.6542869950231847 chr4 191154276 25377149 0.13275742259618614 1.3946999487074094 chr5 180915260 31606626 0.17470403546942365 0.5734221405622515 chr6 171115067 23980690 0.1401436496530139 1.6941688479495154 chr7 159138663 50832892 0.3194251544013537 3.015960269028878 chr8 146364022 25206508 0.1722179238829608 0.8035422925594287 chr9 141213431 24076634 0.17049818724395982 2.5340389798888148 chr10 135534747 27786873 0.20501659991293597 5.258847523634369 chr11 135006516 26359013 0.19524252444230172 1.445103445575972 chr12 133851895 26389897 0.1971574403186447 0.599396317660233 chr13 115169878 17958853 0.15593359402534054 0.5334634653609518 chr14 107349540 15838739 0.14754361313518438 0.5922162528041146 chr15 102531392 18536649 0.18078998673889066 0.5857246343705422 chr16 90354753 19641651 0.21738370531542486 3.3509994378912644 chr17 81195210 10682851 0.13156996576522187 1.115136153259609 chr18 78077248 15688990 0.20094189282900954 2.6713304628692134 chr19 59128983 7219170 0.1220919020372801 1.3836139499143807 chr20 63025520 11772186 0.18678443271868284 0.6693805604114609 chr21 48129895 7018181 0.1458175007445996 0.7308843952532204 chr22 51304566 5652868 0.11018255178301284 0.47290177109444953 chrMT 16571 153082 9.237945808943335 6.520359065959465 chrX 155270560 27021157 0.1740262738796073 0.8696022067664727 chrY 59373566 1533891 0.02583457763005173 1.553047934531321