BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238533.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 = 3,013,783 number of mapped reads = 2,746,267 (91.12%) number of supplementary alignments = 20,801 (0.69%) number of secondary alignments = 0 number of mapped bases = 169,199,000 bp number of sequenced bases = 169,121,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,947 duplication rate = 5.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0624 >>>>>>> ACTG content number of A's = 41,085,149 bp (24.29%) number of C's = 30,631,531 bp (18.11%) number of T's = 55,234,417 bp (32.66%) number of G's = 42,158,773 bp (24.93%) number of N's = 11,599 bp (0.01%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 972,086 number of insertions = 13,210 mapped reads with insertion percentage = 0.48% number of deletions = 44,294 mapped reads with deletion percentage = 1.6% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.0547X std coverageData = 0.678X There is a 4.57% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 13830369 0.055487801573019954 1.0639422018344584 chr2 243199373 14201560 0.05839472291731607 1.54325282795557 chr3 198022430 11163898 0.056376936693484675 0.29129901750878295 chr4 191154276 10432971 0.05457880000549922 0.31300840466692376 chr5 180915260 9771754 0.054012878736708 0.2856078790639839 chr6 171115067 9582325 0.05599930601084941 0.5044042278601861 chr7 159138663 9619589 0.06044784352624604 0.8876593755066003 chr8 146364022 8466184 0.05784334076307359 0.46026604001404203 chr9 141213431 7392588 0.05235045949701484 0.46763702234239657 chr10 135534747 7724231 0.056990780378997574 0.4675186891473052 chr11 135006516 7333665 0.05432082255940891 0.4300590484548524 chr12 133851895 7637286 0.05705773534248432 0.29670923466152876 chr13 115169878 5020205 0.043589566014822036 0.35145341426076987 chr14 107349540 5088323 0.04739957898282564 0.2915962795281831 chr15 102531392 5041016 0.04916558628210178 0.37654483901885527 chr16 90354753 5066338 0.05607162691264288 0.36048167070401765 chr17 81195210 4855419 0.059799328063810664 0.3182320575559488 chr18 78077248 4367288 0.05593547559463161 1.0718439939396023 chr19 59128983 4220613 0.07137976650131121 0.6951169394845934 chr20 63025520 3569657 0.056638279224034964 0.3098965501682025 chr21 48129895 2246897 0.04668402039937964 0.30853425803032797 chr22 51304566 2128338 0.04148437782321363 0.2365084194231239 chrMT 16571 73602 4.44161486935007 3.622095667156942 chrX 155270560 9819854 0.0632435021809672 0.3583136536987264 chrY 59373566 545030 0.009179674335208365 0.2508366948791666