Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F5 I102 R1 278 39.1 2251254 95.8% 2156701 87.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 4,568,721 A→G I145T (ATC→ACC)  mcrB ← 5‑methylcytosine‑specific restriction endonuclease subunit McrB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,568,7210AG100.0% 192.3 / NA 50I145T (ATC→ACC) mcrB5‑methylcytosine‑specific restriction endonuclease subunit McrB
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (29/21);  total (29/21)

CGCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGATTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTAT  >  NZ_CP009273/4568636‑4568807
                                                                                     |                                                                                      
cGCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTAtg                                                                                   >  1:1078200/1‑91 (MQ=255)
 gCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTAtgt                                                                                  <  1:1008408/91‑1 (MQ=255)
 gCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTAtgt                                                                                  <  2:832379/91‑1 (MQ=255)
    tCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTAtgttgt                                                                               >  2:48963/1‑91 (MQ=255)
      ttCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTcc                                                                             <  2:1078200/91‑1 (MQ=255)
      ttCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTcc                                                                             <  2:325479/91‑1 (MQ=255)
          aGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCa                                                                         >  2:569398/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  1:592224/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  2:1073376/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  1:942229/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  2:759678/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  2:626781/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  2:481473/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  1:461435/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  1:108320/1‑91 (MQ=255)
               gTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATagag                                                                    >  1:376731/1‑91 (MQ=255)
                  tGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCa                                                                 <  1:779141/91‑1 (MQ=255)
                       cAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCg                                                            >  2:449078/1‑91 (MQ=255)
                       cAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCg                                                            >  2:370402/1‑91 (MQ=255)
                         gTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAAt                                                              >  2:461748/1‑87 (MQ=255)
                         gTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAAt                                                              <  1:461748/87‑1 (MQ=255)
                         gTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCggg                                                          <  1:485194/91‑1 (MQ=255)
                         gTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCggg                                                          >  2:308017/1‑91 (MQ=255)
                         gTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCggg                                                          >  1:10004/1‑91 (MQ=255)
                           ttttGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGgtg                                                        <  2:108320/91‑1 (MQ=255)
                           ttttGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGgtg                                                        >  2:1060252/1‑91 (MQ=255)
                             ttGACATAGGTGGAATAACACTCTTGGCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTa                                                      <  2:178759/91‑1 (MQ=255)
                             ttGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTa                                                      <  1:1073376/91‑1 (MQ=255)
                             ttGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTa                                                      <  2:706344/91‑1 (MQ=255)
                             ttGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTa                                                      <  2:638470/91‑1 (MQ=255)
                             ttGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTa                                                      <  1:26196/91‑1 (MQ=255)
                                   tAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAAt                                                >  2:406407/1‑91 (MQ=255)
                                              acacTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTgaga                                     >  1:297400/1‑91 (MQ=255)
                                               cacTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGAc                                    >  1:806014/1‑91 (MQ=255)
                                               cacTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGAc                                    >  1:520530/1‑91 (MQ=255)
                                                   ctTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGc                                                                  >  2:385476/1‑57 (MQ=255)
                                                   ctTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGc                                                                  <  1:385476/57‑1 (MQ=255)
                                                        cAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGa                           >  2:206249/1‑91 (MQ=255)
                                                          gAATTAAATCTTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAAc                         >  2:367839/1‑91 (MQ=255)
                                                            aTTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAg                       <  1:48963/91‑1 (MQ=255)
                                                            aTTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAg                       <  1:615198/91‑1 (MQ=255)
                                                              tAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGc                     <  2:520530/91‑1 (MQ=255)
                                                              tAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGc                     <  2:506547/91‑1 (MQ=255)
                                                              tAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGc                     <  1:1060252/91‑1 (MQ=255)
                                                              tAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGc                     <  2:942229/91‑1 (MQ=255)
                                                               aaaTATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCg                    >  1:776719/1‑91 (MQ=255)
                                                                aaTATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGt                   >  2:720513/1‑91 (MQ=255)
                                                                   atTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAAt                <  2:393629/91‑1 (MQ=255)
                                                                         ttATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACt          >  2:65660/1‑91 (MQ=255)
                                                                                 gTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTAt  >  1:607908/1‑91 (MQ=255)
                                                                                     |                                                                                      
CGCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGATTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTAT  >  NZ_CP009273/4568636‑4568807

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AATCATTTAACGCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGATTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTATTTTTTAGGATATAC  >  NZ_CP009273/4568626‑4568821
                                                                                               |                                                                                                    
AATCATTTAACGCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATG                                                                                                 >  SRR3722125.1102465/1‑101 (MQ=60)
           GCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCAT                                                                                      <  SRR3722125.1030963/101‑1 (MQ=60)
               CTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAG                                                                                  >  SRR3722125.963175/1‑101 (MQ=60)
               CTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAG                                                                                  >  SRR3722125.604955/1‑101 (MQ=60)
               CTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAG                                                                                  >  SRR3722125.471158/1‑101 (MQ=60)
               CTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAG                                                                                  >  SRR3722125.384634/1‑101 (MQ=60)
               CTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAG                                                                                  >  SRR3722125.110365/1‑101 (MQ=60)
                         GTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGG                                                                        >  SRR3722125.10196/1‑101 (MQ=60)
                           ctcggagatgtgtataagagacaGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTG                                                                      <  SRR3722125.393563/78‑1 (MQ=60)
                            TGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGT                                                                     <  SRR3722125.796099/101‑1 (MQ=60)
                               TTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAAT                                                                  <  SRR3722125.471480/101‑1 (MQ=60)
                                   GTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAAT                                                              <  SRR3722125.495441/101‑1 (MQ=60)
                                       TTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCC                                                          <  SRR3722125.26658/101‑1 (MQ=60)
                                       TTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCC                                                          <  SRR3722125.1097546/101‑1 (MQ=60)
                                              AGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGA                                                   >  SRR3722125.303479/1‑101 (MQ=60)
                                               GGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGAC                                                  >  SRR3722125.531598/1‑101 (MQ=60)
                                               GGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGAC                                                  >  SRR3722125.823667/1‑101 (MQ=60)
                                                               TGCCAGAATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCG                                  >  SRR3722125.793621/1‑101 (MQ=60)
                                                                      ATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGG                           <  SRR3722125.49878/101‑1 (MQ=60)
                                                                      ATTAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGG                           <  SRR3722125.628463/101‑1 (MQ=60)
                                                                        TAAATATTAATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGAC                         <  SRR3722125.1084115/101‑1 (MQ=60)
                                                                                 ATTTATAGTCGTTGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTAT                >  SRR3722125.620997/1‑101 (MQ=60)
                                                                                             TGGTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACctgtctcttatacacatctcc    >  SRR3722125.138839/1‑80 (MQ=60)
                                                                                               GTTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTATTTTTTAGGATATAC  >  SRR3722125.344365/1‑101 (MQ=60)
                                                                                               |                                                                                                    
AATCATTTAACGCATCTTCCAGACAGTATGATTCAGTTTTTGACATAGGTGGAATAACACTCTTGCCAGAATTAAATATTAATTTATAGTCGTTGATTATGTTGTCCAGCATAGAGGCAAATCGGGTGTAATCAATACCCTGTGAGACTTTTTGGGAACAGGCGTAATAGGACTGTCCGTATTTTTTAGGATATAC  >  NZ_CP009273/4568626‑4568821

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑