BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013288.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 = 1,765,274 number of mapped reads = 1,455,093 (82.43%) number of supplementary alignments = 11,578 (0.66%) number of secondary alignments = 0 number of mapped bases = 93,995,299 bp number of sequenced bases = 93,945,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,562 duplication rate = 4.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1705 >>>>>>> ACTG content number of A's = 25,302,642 bp (26.93%) number of C's = 16,895,362 bp (17.98%) number of T's = 30,380,237 bp (32.34%) number of G's = 21,366,547 bp (22.74%) number of N's = 1,148 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 743,323 number of insertions = 6,626 mapped reads with insertion percentage = 0.45% number of deletions = 28,691 mapped reads with deletion percentage = 1.95% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.2973X There is a 2.39% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.1% 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 6254833 0.025094553325104855 0.29545559584844505 chr2 243199373 8630285 0.03548646073195263 0.4013530863552964 chr3 198022430 4722211 0.023846849066542615 0.1870601523945631 chr4 191154276 7681500 0.04018481909345308 0.25039250280229747 chr5 180915260 2523381 0.013947861556841584 0.14433577594952512 chr6 171115067 3698214 0.021612439306703483 0.20262982615960762 chr7 159138663 5090932 0.03199054148142491 0.528754820372079 chr8 146364022 6090727 0.04161355309025329 0.44037778368519354 chr9 141213431 3012644 0.02133397636942905 0.2815255230380411 chr10 135534747 6111735 0.04509349178185281 0.34927306984173945 chr11 135006516 4346299 0.03219325354636957 0.25972219926864903 chr12 133851895 5752481 0.04297646290327081 0.25742971172907225 chr13 115169878 2740089 0.023791715747063655 0.18804238305404544 chr14 107349540 2982226 0.027780519599804526 0.21102891085490744 chr15 102531392 3502566 0.03416091337177984 0.22770848678879002 chr16 90354753 3962389 0.04385368636888421 0.2646321434557604 chr17 81195210 2115873 0.02605908649044691 0.2000786090862209 chr18 78077248 4884996 0.06256619085754662 0.529177121097843 chr19 59128983 1438204 0.02432316483440955 0.2740485341398989 chr20 63025520 3093831 0.04908854381526721 0.27685823082918615 chr21 48129895 1531765 0.03182564599403344 0.22130810058962902 chr22 51304566 1052385 0.02051250175276797 0.1707655858958906 chrMT 16571 19056 1.1499607748476253 1.2807145478724535 chrX 155270560 2555213 0.016456519510202064 0.17612129138714908 chrY 59373566 201464 0.0033931598449047176 0.08167832126497301