BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008749.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,730,415 number of mapped reads = 1,813,447 (66.42%) number of supplementary alignments = 10,645 (0.39%) number of secondary alignments = 0 number of mapped bases = 107,974,271 bp number of sequenced bases = 107,915,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,741 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8534 >>>>>>> ACTG content number of A's = 29,839,812 bp (27.65%) number of C's = 17,655,797 bp (16.36%) number of T's = 34,040,720 bp (31.54%) number of G's = 26,355,042 bp (24.42%) number of N's = 23,997 bp (0.02%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 1,228,843 number of insertions = 8,401 mapped reads with insertion percentage = 0.46% number of deletions = 39,389 mapped reads with deletion percentage = 2.15% homopolymer indels = 49.2% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.2773X There is a 2.75% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 8199694 0.032897386442218735 0.3341539282181879 chr2 243199373 9519403 0.03914238298632456 0.3106656022985483 chr3 198022430 8673294 0.043799553414226866 0.2736565113408907 chr4 191154276 5716745 0.02990644582808077 0.22638888913845587 chr5 180915260 5682777 0.03141126403599122 0.23095107287961347 chr6 171115067 5989238 0.0350012310721884 0.2673417070361306 chr7 159138663 6468037 0.040644032556689254 0.3602559017466998 chr8 146364022 8579932 0.05862049896387789 0.3879579063556146 chr9 141213431 3725323 0.026380798013469414 0.23984461088966244 chr10 135534747 5663647 0.04178741706730009 0.29499181768744515 chr11 135006516 5038056 0.03731713215975442 0.29127967563032586 chr12 133851895 4885286 0.036497697697892136 0.24702777767504727 chr13 115169878 3269812 0.028391208333137245 0.21797841832800202 chr14 107349540 3900782 0.03633720274907559 0.2594440552258148 chr15 102531392 3153668 0.030758072610581548 0.22803425352012374 chr16 90354753 2729434 0.03020797367461123 0.23510883898776425 chr17 81195210 2673433 0.03292599403339187 0.23868721853930944 chr18 78077248 2039977 0.02612767550413662 0.32926685578044185 chr19 59128983 1809933 0.03060991257028723 0.24948694451556475 chr20 63025520 2384875 0.037839830595606354 0.25053467221913184 chr21 48129895 1196670 0.02486334117288226 0.20510333285229448 chr22 51304566 1261346 0.02458545307643768 0.19282208328121203 chrMT 16571 54310 3.27741234687104 4.52003106628094 chrX 155270560 5103137 0.032866095156738016 0.2423244790469123 chrY 59373566 255462 0.004302621809847164 0.09214045835438775