BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237314.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 = 2,828,738 number of mapped reads = 2,304,239 (81.46%) number of supplementary alignments = 20,534 (0.73%) number of secondary alignments = 0 number of mapped bases = 151,141,070 bp number of sequenced bases = 151,083,048 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 286,660 duplication rate = 9.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9849 >>>>>>> ACTG content number of A's = 40,931,648 bp (27.09%) number of C's = 27,750,457 bp (18.37%) number of T's = 48,088,418 bp (31.83%) number of G's = 34,310,197 bp (22.71%) number of N's = 2,328 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,209,554 number of insertions = 11,544 mapped reads with insertion percentage = 0.5% number of deletions = 33,526 mapped reads with deletion percentage = 1.44% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.5385X There is a 2.8% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% 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% 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 16662025 0.06684847938653682 0.49108988167310025 chr2 243199373 4889706 0.0201057508482968 0.5801494284970502 chr3 198022430 32770405 0.16548834897137663 0.659215322732962 chr4 191154276 14100085 0.07376285425077282 0.5118579929628542 chr5 180915260 24692526 0.13648669548384143 0.6051414671778722 chr6 171115067 8318362 0.04861268002776167 0.37267305894722197 chr7 159138663 2647371 0.01663562424173439 0.33815713930880703 chr8 146364022 8713731 0.05953465121367053 1.1721125265954004 chr9 141213431 12953577 0.091730488440579 0.7212718261886755 chr10 135534747 2275355 0.01678798278938758 0.6063744867757602 chr11 135006516 2186342 0.016194344278908732 0.2685756895222179 chr12 133851895 4346732 0.03247419097054995 0.36282909698662286 chr13 115169878 1614680 0.014019985329844666 0.1756681365047929 chr14 107349540 2278178 0.021222056470852135 0.4373526573991021 chr15 102531392 1338982 0.01305923945712158 0.19316767370468108 chr16 90354753 1287833 0.014253074212930447 0.2774183990829422 chr17 81195210 1365220 0.016814046050253457 0.21305749062251034 chr18 78077248 1521749 0.019490300170415843 0.9497058457225089 chr19 59128983 1011666 0.017109477428353538 0.3599181426460387 chr20 63025520 1068811 0.0169583844766374 0.23739057388618093 chr21 48129895 992787 0.020627242174536223 0.36140479076842313 chr22 51304566 639029 0.012455597032045842 0.16317473441098337 chrMT 16571 284106 17.14477098545652 13.779871319607935 chrX 155270560 2821467 0.01817129403023986 0.2820771280406935 chrY 59373566 360345 0.006069114999762689 0.29404302860046266