BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237249.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 = 1,520,361 number of mapped reads = 1,389,138 (91.37%) number of supplementary alignments = 8,296 (0.55%) number of secondary alignments = 0 number of mapped bases = 96,470,883 bp number of sequenced bases = 96,408,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,727 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2752 >>>>>>> ACTG content number of A's = 28,724,712 bp (29.79%) number of C's = 18,015,188 bp (18.69%) number of T's = 29,644,084 bp (30.75%) number of G's = 20,023,234 bp (20.77%) number of N's = 1,568 bp (0%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 856,464 number of insertions = 8,239 mapped reads with insertion percentage = 0.59% number of deletions = 35,816 mapped reads with deletion percentage = 2.54% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.4539X There is a 2.78% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8811797 0.03535315966173661 1.0436499035622946 chr2 243199373 8111469 0.03335316575836731 0.45093386444962114 chr3 198022430 7286885 0.036798280881615276 0.21123875233145303 chr4 191154276 5081875 0.026585201787481857 0.1979418953746048 chr5 180915260 5466155 0.030213896826613743 0.1951111013082292 chr6 171115067 5782222 0.0337914252752506 0.24459371756728643 chr7 159138663 5945467 0.03736029251420819 0.4928010870577067 chr8 146364022 5762201 0.039368971426598266 0.5108346895621996 chr9 141213431 4364441 0.030906698952736303 0.4488430362375583 chr10 135534747 3850844 0.02841222701363806 0.385414272375272 chr11 135006516 3907091 0.02894001797661381 0.35790549106421565 chr12 133851895 1644353 0.01228486903379291 0.13978342803276553 chr13 115169878 4913231 0.042660729396622264 0.220753259298429 chr14 107349540 4042957 0.03766161457235867 0.24622674074099055 chr15 102531392 1608803 0.015690833496145258 0.13323651966516956 chr16 90354753 2778398 0.03074988207869928 0.2812163074329227 chr17 81195210 3145371 0.038738381241947645 0.3685379307888376 chr18 78077248 2907637 0.03724051595670995 0.934855527494704 chr19 59128983 2134903 0.03610586368448109 0.6211516002308807 chr20 63025520 1180529 0.01873096802691989 0.15670723812436577 chr21 48129895 1472890 0.030602393792880704 0.23128329355906527 chr22 51304566 885413 0.017257976609723197 0.13930388812301875 chrMT 16571 17109 1.0324663568885402 1.2098269746690504 chrX 155270560 5160514 0.033235624319252796 0.23486627777462335 chrY 59373566 208328 0.003508766847522684 0.1310636930501103