BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237325.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 = 3,614,810 number of mapped reads = 3,190,028 (88.25%) number of supplementary alignments = 35,099 (0.97%) number of secondary alignments = 0 number of mapped bases = 196,678,952 bp number of sequenced bases = 196,581,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,271,752 duplication rate = 22.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3453 >>>>>>> ACTG content number of A's = 49,365,304 bp (25.11%) number of C's = 34,917,348 bp (17.76%) number of T's = 64,747,603 bp (32.94%) number of G's = 47,530,491 bp (24.18%) number of N's = 20,656 bp (0.01%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,250,709 number of insertions = 15,330 mapped reads with insertion percentage = 0.48% number of deletions = 55,257 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0635X std coverageData = 0.9209X There is a 1.77% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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% 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 19966440 0.08010587865295629 1.047676388418026 chr2 243199373 9005664 0.037029963888928284 1.6646281651156198 chr3 198022430 12215728 0.06168860769964291 0.6456043356225346 chr4 191154276 13348573 0.06983141198473634 0.7755770041320638 chr5 180915260 11737420 0.06487799868291928 0.6710576449530168 chr6 171115067 25636830 0.14982216615676514 1.1915648221999882 chr7 159138663 6842037 0.042994184260552695 0.647639051118739 chr8 146364022 9150191 0.06251666820142453 1.0682995506025117 chr9 141213431 6478204 0.04587526805435384 0.6670003352872255 chr10 135534747 9612756 0.07092466111291741 0.9083650766111547 chr11 135006516 4833797 0.03580417555549689 0.5545190165217363 chr12 133851895 3847459 0.028744150390997453 0.47720996736943117 chr13 115169878 7280815 0.06321804908050697 0.7098508827967103 chr14 107349540 8379603 0.07805904897217072 0.7417879328807766 chr15 102531392 6320298 0.06164256503998307 0.6620112228357092 chr16 90354753 2177336 0.0240976365681615 0.4555186109725842 chr17 81195210 9907736 0.1220236513951993 0.9669717283230027 chr18 78077248 5967286 0.0764279755352033 1.6926742908707173 chr19 59128983 5806126 0.09819424765009065 0.90501433653583 chr20 63025520 6901927 0.1095100365693135 0.881678009006759 chr21 48129895 2391683 0.04969225467871891 0.654820992055616 chr22 51304566 2008673 0.03915193435219781 0.5184372420589243 chrMT 16571 17966 1.0841832116347836 2.961016787238105 chrX 155270560 6122507 0.0394312160656856 0.5512087601569848 chrY 59373566 721897 0.012158558911553333 0.46983364242183956