BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237590.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 = 1,636,554 number of mapped reads = 1,306,176 (79.81%) number of supplementary alignments = 6,861 (0.42%) number of secondary alignments = 0 number of mapped bases = 81,721,686 bp number of sequenced bases = 81,673,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,772 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6255 >>>>>>> ACTG content number of A's = 21,157,506 bp (25.91%) number of C's = 14,814,991 bp (18.14%) number of T's = 24,962,694 bp (30.56%) number of G's = 20,693,230 bp (25.34%) number of N's = 45,012 bp (0.06%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 806,470 number of insertions = 7,559 mapped reads with insertion percentage = 0.57% number of deletions = 29,242 mapped reads with deletion percentage = 2.21% homopolymer indels = 46.42% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2724X There is a 2.12% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 6998853 0.028079580993300716 0.32148488706077877 chr2 243199373 7141706 0.029365643142509255 0.3866927528429309 chr3 198022430 5679187 0.028679513729833534 0.22101744002981466 chr4 191154276 5126785 0.026820142909070997 0.22897233333769879 chr5 180915260 4537768 0.02508228437999094 0.1994505144199463 chr6 171115067 4299628 0.025127115194362167 0.2195119963238892 chr7 159138663 4720739 0.029664312311081815 0.3850847793116912 chr8 146364022 4448781 0.030395318051590573 0.2759134820545653 chr9 141213431 3243246 0.022966979677733344 0.28069542730174013 chr10 135534747 3610195 0.02663667494801167 0.2713473658613873 chr11 135006516 3398403 0.025172140580236882 0.30594865630343443 chr12 133851895 4916530 0.03673111986946468 0.2575777471225243 chr13 115169878 2693086 0.02338359688112199 0.20094291476806028 chr14 107349540 2330128 0.02170598961113387 0.21188424116058263 chr15 102531392 2517709 0.02455549418464932 0.20874899260619986 chr16 90354753 2220308 0.02457322859374094 0.2265305545692812 chr17 81195210 2035566 0.0250700256825495 0.21380741961145538 chr18 78077248 2053431 0.02629999202840756 0.398659366717849 chr19 59128983 1655428 0.027996896209089205 0.2696829587693291 chr20 63025520 1708197 0.027103259124240466 0.22148201830648448 chr21 48129895 983375 0.020431688039211388 0.20673970719197002 chr22 51304566 870913 0.016975350692957816 0.1683265972613171 chrMT 16571 55889 3.372699293947257 3.0281416539936274 chrX 155270560 4170965 0.026862561711634196 0.22608463376799065 chrY 59373566 304870 0.005134776644542455 0.14101584687070248