BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238297.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 = 2,316,405 number of mapped reads = 1,949,423 (84.16%) number of supplementary alignments = 26,750 (1.15%) number of secondary alignments = 0 number of mapped bases = 124,072,773 bp number of sequenced bases = 123,992,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,388 duplication rate = 5.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.917 >>>>>>> ACTG content number of A's = 33,756,627 bp (27.22%) number of C's = 23,539,951 bp (18.98%) number of T's = 38,420,724 bp (30.99%) number of G's = 28,244,332 bp (22.78%) number of N's = 31,187 bp (0.03%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,155,607 number of insertions = 10,123 mapped reads with insertion percentage = 0.52% number of deletions = 47,236 mapped reads with deletion percentage = 2.39% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.3758X There is a 3% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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% 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 12663230 0.05080520942814421 0.6415695238013758 chr2 243199373 8802330 0.03619388443077935 0.45589134899019446 chr3 198022430 10626052 0.05366085044002338 0.299609594636592 chr4 191154276 7456260 0.039006503835676685 0.3150932822848574 chr5 180915260 6537323 0.036134724069158124 0.24349047332468596 chr6 171115067 7634946 0.044618782751608896 0.3265542042496175 chr7 159138663 7852998 0.049346889385390905 0.39700001712554805 chr8 146364022 6095973 0.04164939523184188 0.5650672240298774 chr9 141213431 6007162 0.04253959384359127 0.3141739084111624 chr10 135534747 5544910 0.04091135389805243 0.4463001757900145 chr11 135006516 5335284 0.03951871478558857 0.29017137201324494 chr12 133851895 3996972 0.029861153628045384 0.22371592095360543 chr13 115169878 4448036 0.038621522200448975 0.2540927008411853 chr14 107349540 3234323 0.030128894823396542 0.24147774030153019 chr15 102531392 3368754 0.03285583014419623 0.24842759663115171 chr16 90354753 4386488 0.048547396283624394 0.29975306998610785 chr17 81195210 4689700 0.057758333280990344 0.32082312307812355 chr18 78077248 2463281 0.03154928052792025 0.43710863868921396 chr19 59128983 2888918 0.04885790103983355 0.4797032338771478 chr20 63025520 2391748 0.03794888165936592 0.26096348455859564 chr21 48129895 1650920 0.03430134223230697 0.2838052078055899 chr22 51304566 1631964 0.03180933252607575 0.2268026836468262 chrMT 16571 2830 0.1707802788003138 0.5259939088225896 chrX 155270560 3961821 0.025515596775074426 0.21643346922247636 chrY 59373566 400550 0.006746268196186835 0.26109735318806715