BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819026.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 590,755 number of mapped reads = 579,557 (98.1%) number of supplementary alignments = 6,808 (1.15%) number of secondary alignments = 0 number of mapped bases = 53,644,767 bp number of sequenced bases = 53,613,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,603 duplication rate = 15.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.047 >>>>>>> ACTG content number of A's = 15,505,860 bp (28.92%) number of C's = 11,810,181 bp (22.03%) number of T's = 14,848,203 bp (27.69%) number of G's = 11,446,855 bp (21.35%) number of N's = 2,424 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 357,997 number of insertions = 7,923 mapped reads with insertion percentage = 1.33% number of deletions = 16,184 mapped reads with deletion percentage = 2.74% homopolymer indels = 40.9% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.2796X There is a 1.32% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 5429876 0.021784804299444453 0.5708059132932306 chr2 243199373 4402764 0.01810351706786678 0.34658604142620864 chr3 198022430 2797789 0.014128646941662115 0.14827310554883666 chr4 191154276 2965998 0.015516252432668574 0.18068832670696364 chr5 180915260 2919239 0.016135946741032237 0.16358337171436077 chr6 171115067 2296781 0.013422435792869135 0.17132938522833488 chr7 159138663 2657985 0.016702320793030665 0.3370814920642226 chr8 146364022 4723698 0.03227362800948446 0.24746887952249824 chr9 141213431 2268145 0.016061822051473277 0.25511862114356954 chr10 135534747 2907569 0.021452572601179533 0.3389093610465601 chr11 135006516 1818704 0.01347123127005218 0.1769948834407065 chr12 133851895 2438121 0.01821506524057803 0.1692560522639045 chr13 115169878 1097713 0.009531250870995973 0.12077937152099098 chr14 107349540 1234866 0.011503225817269454 0.14272083458962767 chr15 102531392 1411720 0.013768661211582888 0.14588832380099218 chr16 90354753 1771073 0.019601326340851155 0.2766769631780763 chr17 81195210 1902611 0.02343255224045852 0.21198720123317888 chr18 78077248 1283203 0.016435043919580773 0.29799822346601873 chr19 59128983 1189420 0.02011568506091167 0.47255600904440753 chr20 63025520 1592646 0.02526985893968031 0.20816877789772154 chr21 48129895 734722 0.015265397940303007 0.16507398732176498 chr22 51304566 429254 0.008366779674152199 0.12204698329798569 chrMT 16571 3583 0.21622110916661638 0.5741331340224181 chrX 155270560 3154884 0.020318623182656134 0.20381076229028247 chrY 59373566 212403 0.003577400084071083 0.2330921484569515