BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240032.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 = 2,356,669 number of mapped reads = 1,867,487 (79.24%) number of supplementary alignments = 16,295 (0.69%) number of secondary alignments = 0 number of mapped bases = 123,918,433 bp number of sequenced bases = 123,857,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 280,383 duplication rate = 11.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9735 >>>>>>> ACTG content number of A's = 35,171,223 bp (28.4%) number of C's = 22,985,301 bp (18.56%) number of T's = 39,522,917 bp (31.91%) number of G's = 26,167,043 bp (21.13%) number of N's = 11,303 bp (0.01%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,032,721 number of insertions = 8,799 mapped reads with insertion percentage = 0.47% number of deletions = 34,534 mapped reads with deletion percentage = 1.83% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.4757X There is a 1.7% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 10044912 0.04030044924140831 0.6574927117580148 chr2 243199373 13126964 0.05397614244671593 0.5426546844637334 chr3 198022430 7699971 0.03888433749651492 0.38608128180619106 chr4 191154276 8035213 0.04203522499282203 0.4124971669515323 chr5 180915260 7230981 0.03996888377464676 0.388825793331872 chr6 171115067 6154682 0.035968089239038194 0.40737690658241815 chr7 159138663 7375075 0.0463437034154296 0.6607908036254588 chr8 146364022 6885767 0.04704548908884179 0.6928966359058928 chr9 141213431 4584037 0.03246176349896916 0.4000800870505446 chr10 135534747 5692851 0.042002889487815255 0.4679406251263902 chr11 135006516 5231542 0.038750292615506055 0.4340193356429582 chr12 133851895 6312306 0.04715888407855563 0.4293471375301184 chr13 115169878 3180781 0.02761816766012377 0.33007674016142313 chr14 107349540 4083450 0.038038821591596945 0.39669802847907903 chr15 102531392 3418813 0.033344061104720005 0.3535634454391908 chr16 90354753 3715917 0.04112586086091121 0.39855993306825344 chr17 81195210 3201391 0.03942832341957118 0.39859511512460655 chr18 78077248 3026886 0.03876783669424414 0.5889639261330029 chr19 59128983 2320109 0.03923810088193128 0.48850526278441314 chr20 63025520 2447694 0.03883655382771931 0.3852367417166981 chr21 48129895 2012679 0.04181764784652034 0.40545951252256807 chr22 51304566 1136939 0.022160581184918315 0.2849261114908537 chrMT 16571 25354 1.5300223281636594 2.9037482562936616 chrX 155270560 6652083 0.0428418819382116 0.4229145395079027 chrY 59373566 322036 0.00542389520615959 0.12932694813307374