BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013175.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 = 2,877,687 number of mapped reads = 2,606,016 (90.56%) number of supplementary alignments = 16,895 (0.59%) number of secondary alignments = 0 number of mapped bases = 169,562,332 bp number of sequenced bases = 169,489,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,088 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3754 >>>>>>> ACTG content number of A's = 46,993,041 bp (27.73%) number of C's = 32,617,236 bp (19.24%) number of T's = 51,281,596 bp (30.26%) number of G's = 38,558,155 bp (22.75%) number of N's = 39,919 bp (0.02%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,337,799 number of insertions = 11,613 mapped reads with insertion percentage = 0.44% number of deletions = 41,492 mapped reads with deletion percentage = 1.58% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.4372X There is a 4.8% of reference with a coverageData >= 1X There is a 0.48% 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 0.01% 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 12584746 0.050490329570733544 0.7191257587129776 chr2 243199373 16298776 0.06701816620226238 0.5376963263931063 chr3 198022430 10936967 0.055230950352442396 0.26015155745564483 chr4 191154276 10542647 0.055152556461776456 0.2739927507903781 chr5 180915260 9476278 0.0523796500085178 0.254980666075997 chr6 171115067 9178720 0.05364063002120088 0.32770268217040865 chr7 159138663 10117467 0.06357642328564743 0.7898935421126027 chr8 146364022 8972836 0.06130492915806864 0.3660939890868812 chr9 141213431 6290993 0.044549537217886875 0.37940802020199443 chr10 135534747 7929278 0.058503654417121534 0.4568713611393585 chr11 135006516 7299236 0.054065805238615296 0.34821303441611273 chr12 133851895 8164016 0.06099290562901631 0.2762706947929004 chr13 115169878 4468762 0.03880148245012468 0.21919263340915207 chr14 107349540 5578606 0.0519667434066322 0.2910445470748451 chr15 102531392 4785802 0.04667645592873644 0.24301488576098318 chr16 90354753 5412480 0.05990254879010073 0.3140242667631043 chr17 81195210 4496706 0.05538141966749024 0.3029031381148919 chr18 78077248 4163016 0.0533191948568679 0.745162527529336 chr19 59128983 3501781 0.05922275037268948 0.6023060286264649 chr20 63025520 3721883 0.05905358654716375 0.27634359307670514 chr21 48129895 2647673 0.05501098641499218 0.2778369800502863 chr22 51304566 1828070 0.035631721355951045 0.207160742570323 chrMT 16571 341494 20.6079295154185 13.592276908578674 chrX 155270560 10406007 0.06701854491926866 0.3255823312886378 chrY 59373566 418092 0.007041719542329662 0.14471359963510194