BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231756.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 = 4,459,544 number of mapped reads = 4,020,814 (90.16%) number of supplementary alignments = 37,784 (0.85%) number of secondary alignments = 0 number of mapped bases = 276,294,023 bp number of sequenced bases = 276,208,866 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 874,958 duplication rate = 10.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9036 >>>>>>> ACTG content number of A's = 69,518,394 bp (25.17%) number of C's = 48,453,776 bp (17.54%) number of T's = 75,019,795 bp (27.16%) number of G's = 83,157,447 bp (30.11%) number of N's = 59,454 bp (0.02%) GC percentage = 47.65% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,668,411 number of insertions = 17,518 mapped reads with insertion percentage = 0.43% number of deletions = 52,369 mapped reads with deletion percentage = 1.29% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.0893X std coverageData = 57.8297X There is a 3.09% of reference with a coverageData >= 1X There is a 1.73% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 4277641 0.017162007391748887 1.6177610590339717 chr2 243199373 61096781 0.2512209642908907 206.30277184827264 chr3 198022430 17559554 0.08867457085543289 0.6375084094938425 chr4 191154276 9366129 0.0489977477668352 0.4630096792927722 chr5 180915260 17250833 0.09535311172755687 0.7148677944627928 chr6 171115067 26149919 0.15282066891280824 0.898195001969159 chr7 159138663 10286377 0.06463782468751796 1.190805040860059 chr8 146364022 13890597 0.0949044499474058 0.8540451999012185 chr9 141213431 2107084 0.01492127190082932 0.44586832210280686 chr10 135534747 3245992 0.023949519011534363 0.3370494768720796 chr11 135006516 4128524 0.030580183255747448 0.5488684236319067 chr12 133851895 5102196 0.03811822014174696 0.4209984192265592 chr13 115169878 2390280 0.020754385100590276 0.2911746835310128 chr14 107349540 13726083 0.12786345428215157 0.8377421198730884 chr15 102531392 4844607 0.04724998759404339 0.4825862591991483 chr16 90354753 9499081 0.10513094977969781 0.7228333135774647 chr17 81195210 6362299 0.07835805831403109 0.6871589337891336 chr18 78077248 4280292 0.054821245748825576 0.9358863816984059 chr19 59128983 10554999 0.17850804232503034 1.1488819306707554 chr20 63025520 6777315 0.10753286922503773 0.7425672880245211 chr21 48129895 7727952 0.16056448907690324 0.8775608185080659 chr22 51304566 503892 0.009821581962120097 0.1739159687952654 chrMT 16571 183909 11.098243920101382 12.489194129874722 chrX 155270560 33956987 0.2186955917464328 1.0785242526035925 chrY 59373566 1024700 0.017258522083716515 0.2724219569727553