BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240191.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 = 1,752,603 number of mapped reads = 1,349,813 (77.02%) number of supplementary alignments = 5,663 (0.32%) number of secondary alignments = 0 number of mapped bases = 80,274,484 bp number of sequenced bases = 80,229,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,285 duplication rate = 12.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0206 >>>>>>> ACTG content number of A's = 20,822,906 bp (25.95%) number of C's = 13,271,957 bp (16.54%) number of T's = 27,192,509 bp (33.89%) number of G's = 18,922,470 bp (23.59%) number of N's = 19,291 bp (0.02%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 784,242 number of insertions = 5,593 mapped reads with insertion percentage = 0.41% number of deletions = 27,204 mapped reads with deletion percentage = 1.99% homopolymer indels = 50.42% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.284X There is a 1.73% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 6097542 0.024463497725849197 0.3160109884157257 chr2 243199373 9116862 0.03748719368614491 0.3653693701017818 chr3 198022430 5669777 0.02863199386049348 0.24357659572010454 chr4 191154276 5665669 0.02963924803858429 0.2514893384944236 chr5 180915260 3952291 0.021846089710729762 0.21097649348378297 chr6 171115067 4089532 0.023899309813553708 0.24614566408921834 chr7 159138663 5153308 0.03238250154206712 0.520222142096693 chr8 146364022 5034432 0.03439664974497626 0.3810215698301759 chr9 141213431 2762949 0.01956576637529613 0.24342910803336934 chr10 135534747 3300305 0.02435025019820194 0.24025418879166946 chr11 135006516 3584621 0.026551466597360383 0.2653928283288137 chr12 133851895 3774309 0.028197650843867394 0.23822960591489103 chr13 115169878 1995640 0.017327794686037613 0.1871377098655087 chr14 107349540 2745552 0.025575815229389898 0.23065492593056103 chr15 102531392 2221616 0.02166766642551776 0.22075538292519925 chr16 90354753 2070110 0.022910914271438494 0.21112400163172068 chr17 81195210 1906385 0.02347903281486679 0.223825450526061 chr18 78077248 1787319 0.022891675177895615 0.3153102624593715 chr19 59128983 1280594 0.021657636154506495 0.2600684358903752 chr20 63025520 1561688 0.024778661088397207 0.22659505792375534 chr21 48129895 1347094 0.027988716784027888 0.23922052504173025 chr22 51304566 653784 0.012743193266657786 0.1524851044043 chrMT 16571 52610 3.174823486814314 4.31457901866694 chrX 155270560 4277945 0.027551552593099427 0.2501893120841332 chrY 59373566 172550 0.0029061754518837557 0.07137004579568845