BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240028.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 = 2,119,093 number of mapped reads = 1,670,444 (78.83%) number of supplementary alignments = 14,492 (0.68%) number of secondary alignments = 0 number of mapped bases = 111,075,323 bp number of sequenced bases = 111,022,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,974 duplication rate = 9.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0427 >>>>>>> ACTG content number of A's = 31,936,739 bp (28.77%) number of C's = 20,720,521 bp (18.66%) number of T's = 35,240,466 bp (31.74%) number of G's = 23,114,097 bp (20.82%) number of N's = 10,200 bp (0.01%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 931,529 number of insertions = 8,155 mapped reads with insertion percentage = 0.48% number of deletions = 30,429 mapped reads with deletion percentage = 1.8% homopolymer indels = 48.94% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.4362X There is a 1.6% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 8623374 0.03459720166554771 0.6118562457012068 chr2 243199373 11853612 0.04874030657965553 0.5009336080360066 chr3 198022430 7105263 0.03588110195395542 0.3654545173058213 chr4 191154276 7463139 0.03904249047507574 0.38204529519409547 chr5 180915260 6120201 0.033829103194501116 0.3541227522808273 chr6 171115067 5897424 0.034464668152220636 0.37872663547854135 chr7 159138663 6602606 0.04148964101828605 0.5665518250079523 chr8 146364022 6266318 0.042813239991450903 0.5810355673974764 chr9 141213431 4083281 0.028915670209868353 0.3772751101420088 chr10 135534747 5065512 0.037374268312169424 0.4264527980131457 chr11 135006516 4827490 0.0357574592918167 0.41617898921267416 chr12 133851895 5346371 0.039942437871350274 0.3808330650483271 chr13 115169878 2995838 0.026012339789054914 0.31487335852623677 chr14 107349540 3510197 0.032698761447883244 0.35029610528278854 chr15 102531392 3135509 0.03058096587628499 0.33426420806452684 chr16 90354753 3258101 0.0360589885072233 0.3660531637044616 chr17 81195210 2617745 0.03224014076692455 0.34788950893258164 chr18 78077248 2748085 0.03519700130824283 0.6355129866328254 chr19 59128983 1876523 0.031736094632305784 0.44336023281217773 chr20 63025520 2216720 0.0351717843819456 0.3576875773086136 chr21 48129895 1900056 0.03947766767411398 0.3850166182327303 chr22 51304566 990191 0.019300250975712377 0.250813964255574 chrMT 16571 15968 0.9636111278739967 1.855255139989906 chrX 155270560 6249706 0.04025042480686616 0.39520176515753325 chrY 59373566 306093 0.005155375036762993 0.12845999824225568