BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068942.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 = 2,171,896 number of mapped reads = 1,792,920 (82.55%) number of supplementary alignments = 11,969 (0.55%) number of secondary alignments = 0 number of mapped bases = 119,585,818 bp number of sequenced bases = 119,534,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,580 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4764 >>>>>>> ACTG content number of A's = 33,116,408 bp (27.7%) number of C's = 21,025,847 bp (17.59%) number of T's = 39,489,075 bp (33.04%) number of G's = 25,607,362 bp (21.42%) number of N's = 295,689 bp (0.25%) GC percentage = 39.01% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 1,326,908 number of insertions = 11,348 mapped reads with insertion percentage = 0.63% number of deletions = 30,950 mapped reads with deletion percentage = 1.71% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3722X There is a 3.35% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 10296557 0.04131005555247945 0.6209493631590008 chr2 243199373 9115663 0.03748226357475025 0.36994276822353084 chr3 198022430 7263404 0.036679703405316254 0.21164426409402776 chr4 191154276 9267117 0.048479778710260185 0.27754464383298894 chr5 180915260 6399931 0.03537529669968139 0.21196705075898098 chr6 171115067 6215012 0.03632065901011511 0.2626119837013531 chr7 159138663 6338826 0.03983209284597295 0.4748554917046463 chr8 146364022 7595796 0.0518966061208676 0.750645712994471 chr9 141213431 6745569 0.04776860778915569 0.3737721554626919 chr10 135534747 5323499 0.03927774329338587 0.3625893304468003 chr11 135006516 4820305 0.035704239638329756 0.3056745028145161 chr12 133851895 6491669 0.0484988949913634 0.2497550292265254 chr13 115169878 3984025 0.03459259547014541 0.20650207921663782 chr14 107349540 3111716 0.02898676603551352 0.20125837075170352 chr15 102531392 3160373 0.030823467216752505 0.1942234378483354 chr16 90354753 2788594 0.03086272617003336 0.22574824238867436 chr17 81195210 2572666 0.03168494791749415 0.21716895818280946 chr18 78077248 3835352 0.049122530548207845 0.5879404519200775 chr19 59128983 1676664 0.028356043262235713 0.3935819303272445 chr20 63025520 1927485 0.030582611615104484 0.20670559709148206 chr21 48129895 1454807 0.030226681358851915 0.21997151425613912 chr22 51304566 1002184 0.01953401184604115 0.15238766761793415 chrMT 16571 61373 3.7036388872126005 2.7534675558150012 chrX 155270560 7771227 0.05004958441574501 0.28839698537771935 chrY 59373566 366004 0.006164426775376773 0.16825441377359784