BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240033.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 = 2,457,140 number of mapped reads = 1,813,616 (73.81%) number of supplementary alignments = 17,555 (0.71%) number of secondary alignments = 0 number of mapped bases = 120,251,528 bp number of sequenced bases = 120,187,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 236,074 duplication rate = 9.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.728 >>>>>>> ACTG content number of A's = 33,928,556 bp (28.23%) number of C's = 22,157,099 bp (18.44%) number of T's = 38,504,716 bp (32.04%) number of G's = 25,586,168 bp (21.29%) number of N's = 10,960 bp (0.01%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,034,044 number of insertions = 8,615 mapped reads with insertion percentage = 0.47% number of deletions = 36,576 mapped reads with deletion percentage = 1.99% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.4775X There is a 1.92% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% 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 7909619 0.031733597967645584 0.8475575571563505 chr2 243199373 12788939 0.05258623343572518 0.49341522016075706 chr3 198022430 11631044 0.058735992685273075 0.421229134016001 chr4 191154276 10563663 0.05526249907169223 0.4161788286014336 chr5 180915260 5273348 0.029148165831892787 0.30133612399768056 chr6 171115067 5015124 0.029308488655765186 0.3214011507501308 chr7 159138663 8655157 0.05438751863838394 0.6565462429192275 chr8 146364022 6076498 0.04151633657621133 0.7381720986003323 chr9 141213431 3981211 0.028192863609411204 0.35480572082540224 chr10 135534747 4579854 0.033790995308383906 0.40650730528041606 chr11 135006516 4724278 0.0349929628581779 0.390840487473346 chr12 133851895 8408150 0.06281681704991925 0.4423433334911821 chr13 115169878 2611456 0.02267481780262023 0.2785087987338044 chr14 107349540 4754926 0.04429386469657905 0.3726028505320285 chr15 102531392 2758129 0.026900337020685332 0.2920615508780159 chr16 90354753 2849153 0.03153296207892904 0.3154275040868614 chr17 81195210 2473153 0.030459346062409347 0.3153710493346456 chr18 78077248 2281490 0.029220932582050024 0.5779905179217882 chr19 59128983 2782832 0.0470637555190151 0.5901054314207819 chr20 63025520 2114618 0.03355177394807691 0.3289003482653201 chr21 48129895 1554341 0.03229470997183767 0.323787413672497 chr22 51304566 873473 0.017025248785848806 0.2181915804220091 chrMT 16571 19791 1.194315370225092 1.880826090930666 chrX 155270560 5280829 0.03401049754699152 0.3386075700949744 chrY 59373566 290452 0.004891941306001395 0.11453012731739927