BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004084.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 = 4,263,413 number of mapped reads = 3,884,074 (91.1%) number of supplementary alignments = 44,356 (1.04%) number of secondary alignments = 0 number of mapped bases = 258,924,263 bp number of sequenced bases = 258,813,160 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 519,354 duplication rate = 9.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1044 >>>>>>> ACTG content number of A's = 72,378,016 bp (27.97%) number of C's = 48,513,261 bp (18.74%) number of T's = 81,035,696 bp (31.31%) number of G's = 56,615,913 bp (21.88%) number of N's = 270,274 bp (0.1%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,068,019 number of insertions = 17,930 mapped reads with insertion percentage = 0.46% number of deletions = 63,429 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.0836X std coverageData = 0.6577X There is a 4.25% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% 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 17403180 0.06982201259992046 0.6361127902673962 chr2 243199373 21256509 0.0874036340545993 0.7637708179800393 chr3 198022430 21496356 0.1085551571102324 0.5596435683894964 chr4 191154276 20716435 0.10837547259471193 0.5772837500468014 chr5 180915260 9598203 0.0530535843134515 0.3869132864128245 chr6 171115067 19367636 0.1131848664150656 0.6148833687819218 chr7 159138663 16776055 0.10541784556779894 0.7742883459272312 chr8 146364022 14652384 0.10010919213466271 1.4040070440710481 chr9 141213431 8635466 0.061151874427581895 0.5234420911321029 chr10 135534747 7925632 0.05847675356637512 0.49913919568367215 chr11 135006516 17406432 0.128930310297023 0.8670516491942027 chr12 133851895 14275954 0.10665485161790202 0.562705742050238 chr13 115169878 9842710 0.08546253734852441 0.5008150770393869 chr14 107349540 7636855 0.0711400812709584 0.4855395054635546 chr15 102531392 7224991 0.07046613587378195 0.45028427047715425 chr16 90354753 7211484 0.0798130010935894 0.4943458850358614 chr17 81195210 6726081 0.0828383965014685 0.5506463833093649 chr18 78077248 5523754 0.07074729375707504 0.9307161835925976 chr19 59128983 4440281 0.0750948312437574 0.5792556633288929 chr20 63025520 8892890 0.14109982749844824 0.6793015760907878 chr21 48129895 5229954 0.10866331621957621 0.5761549669081959 chr22 51304566 3428244 0.06682142092382187 0.42506462549824187 chrMT 16571 34880 2.104882022810935 2.67297581906172 chrX 155270560 2849550 0.018352158966902676 0.2691677357984854 chrY 59373566 372347 0.006271258829223766 0.150202081620019