BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549132.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 14,159,759 number of mapped reads = 12,303,453 (86.89%) number of secondary alignments = 0 number of mapped bases = 488,584,832 bp number of sequenced bases = 488,532,420 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 779,103 duplication rate = 5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2329 >>>>>>> ACTG content number of A's = 141,815,621 bp (29.03%) number of C's = 101,856,913 bp (20.85%) number of T's = 143,224,608 bp (29.32%) number of G's = 101,528,079 bp (20.78%) number of N's = 107,199 bp (0.02%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,607,276 number of insertions = 12,146 mapped reads with insertion percentage = 0.1% number of deletions = 41,080 mapped reads with deletion percentage = 0.33% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.1578X std coverageData = 1.2411X There is a 10.32% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 1.16% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 40007867 0.16051260710800797 1.861762203709153 chr2 243199373 41914064 0.17234445748344918 0.9057363946601138 chr3 198022430 33408565 0.16871101420177503 0.5781090129610192 chr4 191154276 31505774 0.16481856780436344 0.6843082941055675 chr5 180915260 29939496 0.1654890582474911 0.587201423073613 chr6 171115067 28692597 0.16768013187289932 0.631804926241748 chr7 159138663 27338079 0.17178778861551702 1.3232584715732254 chr8 146364022 25439462 0.17380953086954662 3.7974255191764104 chr9 141213431 20867212 0.14777073152482217 0.7942168191991625 chr10 135534747 23698931 0.17485502075714945 0.9681450906713017 chr11 135006516 22961937 0.1700802130172739 0.8239818048636837 chr12 133851895 22652524 0.16923573625909444 0.6035872919065267 chr13 115169878 15591527 0.13537851451053895 0.5108978710105772 chr14 107349540 15200352 0.14159680609716632 0.6719599385600761 chr15 102531392 14653848 0.14292059938091936 0.5215867071382048 chr16 90354753 14569666 0.16124958030708136 0.6418953524206059 chr17 81195210 13547672 0.16685309392019554 0.6253719964659982 chr18 78077248 13022396 0.16678861427083086 1.6117182719082306 chr19 59128983 9965883 0.16854480652914325 1.4964435747691984 chr20 63025520 10852214 0.1721876154294324 0.6455215965232077 chr21 48129895 6580673 0.13672735001811245 0.6721381341083874 chr22 51304566 6071993 0.11835190263572253 0.5131224605431297 chrMT 16571 177026 10.68287972964818 13.712144797669666 chrX 155270560 15468866 0.09962523481592389 0.5788651659159288 chrY 59373566 4456208 0.07505373687677779 0.8431106656180554