BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004025.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 = 3,292,018 number of mapped reads = 2,983,964 (90.64%) number of supplementary alignments = 27,675 (0.84%) number of secondary alignments = 0 number of mapped bases = 193,674,374 bp number of sequenced bases = 193,591,827 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,912 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5036 >>>>>>> ACTG content number of A's = 53,341,689 bp (27.55%) number of C's = 38,315,282 bp (19.79%) number of T's = 56,834,108 bp (29.36%) number of G's = 45,064,048 bp (23.28%) number of N's = 36,700 bp (0.02%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,603,295 number of insertions = 15,727 mapped reads with insertion percentage = 0.52% number of deletions = 49,962 mapped reads with deletion percentage = 1.66% homopolymer indels = 44.31% >>>>>>> Coverage mean coverageData = 0.0626X std coverageData = 0.4457X There is a 5.4% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 16597111 0.0665880427234723 0.7826002175713488 chr2 243199373 17560709 0.07220704882327143 0.6589567640329422 chr3 198022430 11070867 0.055907136378439554 0.264449461679259 chr4 191154276 13523983 0.07074904774821777 0.3052530183811648 chr5 180915260 11324648 0.0625964222144666 0.2794789063719555 chr6 171115067 12641537 0.07387740437842333 0.35292619162640765 chr7 159138663 12881175 0.08094308923532932 0.6507529157873051 chr8 146364022 11283926 0.0770949434554347 0.45510473089813785 chr9 141213431 5323380 0.037697405709234556 0.33753429386076256 chr10 135534747 8395275 0.061941864989057016 0.4340773307730019 chr11 135006516 8828323 0.06539182893957504 0.36793065637154804 chr12 133851895 7766063 0.0580198210865823 0.2711732111712853 chr13 115169878 3849084 0.03342092625990278 0.2062913300602528 chr14 107349540 5356968 0.049902104843672364 0.2731808104417071 chr15 102531392 6289145 0.061338726387329255 0.2937397013449908 chr16 90354753 5131809 0.05679622631473521 0.3043507624338186 chr17 81195210 5364951 0.06607472288082018 0.3124667624800193 chr18 78077248 5466965 0.07001994998594213 0.6360158936481121 chr19 59128983 4511039 0.07629150327175423 0.6047201177024689 chr20 63025520 4922406 0.078101791147459 0.3293932788838425 chr21 48129895 2513890 0.052231362648931606 0.267511132256208 chr22 51304566 2217034 0.0432131908103462 0.23178481525294342 chrMT 16571 75893 4.579868444873575 4.199249597156165 chrX 155270560 10352672 0.0666750477360293 0.31664509057756984 chrY 59373566 425521 0.007166842564248204 0.1239215728268089