BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,083,784 number of mapped reads = 5,029,109 (98.92%) number of supplementary alignments = 41,262 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,527,132 number of mapped paired reads (second in pair) = 2,501,977 number of mapped paired reads (both in pair) = 5,001,360 number of mapped paired reads (singletons) = 27,749 number of mapped bases = 674,453,665 bp number of sequenced bases = 674,032,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 823,391 duplication rate = 12.59% >>>>>>> Insert size mean insert size = 36,043.8514 std insert size = 1,814,619.4661 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.87 >>>>>>> ACTG content number of A's = 192,454,531 bp (28.55%) number of C's = 133,223,378 bp (19.77%) number of T's = 196,250,054 bp (29.12%) number of G's = 152,104,842 bp (22.57%) number of N's = 189 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 5,294,739 number of insertions = 101,581 mapped reads with insertion percentage = 1.9% number of deletions = 206,321 mapped reads with deletion percentage = 3.95% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.2179X std coverageData = 2.5594X There is a 11.28% of reference with a coverageData >= 1X There is a 5.26% of reference with a coverageData >= 2X There is a 2.04% of reference with a coverageData >= 3X There is a 1.07% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 61224675 0.2456349948271543 1.2407689478188926 chr2 243199373 56104724 0.2306943612062684 2.1117388367111207 chr3 198022430 43660973 0.2204849874834886 0.7767807930206255 chr4 191154276 38001726 0.19880133887248225 1.3895131735661732 chr5 180915260 43566045 0.24080912245876882 0.819046538853475 chr6 171115067 35321538 0.20641980054275408 0.835060682484769 chr7 159138663 41917629 0.26340317437504174 1.6559190525386198 chr8 146364022 34103460 0.23300439229525954 0.8471964802434384 chr9 141213431 28015013 0.1983877369285079 1.8753572877024873 chr10 135534747 38735813 0.2857998694607812 9.251145921250322 chr11 135006516 31937377 0.236561744916075 1.796828621323329 chr12 133851895 37727291 0.28185847499581534 0.8897887481253487 chr13 115169878 17194520 0.14929702365404954 0.6079452174653228 chr14 107349540 17061403 0.15893317288551026 0.6699042447977188 chr15 102531392 21831220 0.21292230188389522 0.7599392631164928 chr16 90354753 25157773 0.27843331053099113 6.3067294112197665 chr17 81195210 17139738 0.21109296964685478 1.816602407923112 chr18 78077248 14395573 0.1843760297494092 2.024738492726022 chr19 59128983 7124537 0.12049145171328247 0.8157313085033013 chr20 63025520 17021663 0.27007572488096887 0.9263235788928197 chr21 48129895 6516111 0.13538593840688828 0.8663656500368097 chr22 51304566 5786936 0.1127957305008681 0.6339497524366436 chrMT 16571 179022 10.80333112063243 7.464753602706509 chrX 155270560 29970295 0.19301981650610392 0.9602215376363696 chrY 59373566 4758610 0.08014694620161437 2.124617215072063