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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,277,534 G→A 23.7% F405F (TTC→TTT)  btuB ← vitamin B12/cobalamin outer membrane transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,277,5340GA23.7% 86.7 / 19.7 67F405F (TTC→TTT) btuBvitamin B12/cobalamin outer membrane transporter
Reads supporting (aligned to +/- strand):  ref base G (25/26);  new base A (5/11);  total (30/37)
Fisher's exact test for biased strand distribution p-value = 2.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

TTCCGTAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCAT  >  minE/2277470‑2277586
                                                                |                                                    
ttCCGTAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGc                                                  <  1:3027767/69‑1 (MQ=255)
ttCCGTAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGc                                                  <  1:2817289/69‑1 (MQ=255)
ttCCGTAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGc                                                  <  1:2283053/69‑1 (MQ=255)
 tCCGTAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGc                                                  <  1:3034139/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTTGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:3056488/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:1025027/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:348678/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:2804215/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:2275669/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:1953601/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:160222/68‑1 (MQ=255)
     tAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:1400082/68‑1 (MQ=255)
       gAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:2031723/66‑1 (MQ=255)
           ccATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTc                                        <  1:795379/68‑1 (MQ=255)
            cATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCg                                       >  1:2643005/1‑68 (MQ=255)
            cATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCg                                       >  1:2700833/1‑68 (MQ=255)
            cATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCg                                       >  1:249640/1‑68 (MQ=255)
            cATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCg                                       >  1:416305/1‑68 (MQ=255)
            cATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCg                                       >  1:1318286/1‑68 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGGGATa                                              >  1:1224395/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGAt                                               >  1:787988/1‑56 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              >  1:1687879/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              >  1:2976328/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:1850190/57‑1 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              >  1:1537269/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              <  1:2296288/57‑1 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              >  1:3063383/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              >  1:2432025/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATa                                              >  1:2435945/1‑57 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGaa                                  >  1:2067452/1‑69 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGaa                                  >  1:564312/1‑69 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGaa                                  >  1:721936/1‑69 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGaa                                  >  1:1344595/1‑69 (MQ=255)
                cAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGaa                                  >  1:2135395/1‑69 (MQ=255)
                     gCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTccc                             <  1:1478500/69‑1 (MQ=255)
                       cccAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCa                            <  1:858752/68‑1 (MQ=255)
                       cccAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCa                            <  1:2651555/68‑1 (MQ=255)
                       cccAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCa                            <  1:3296656/68‑1 (MQ=255)
                       cccAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCa                            <  1:2339538/68‑1 (MQ=255)
                         aaGATTTGGTGCCTTATAAGATGTTCCGTAGGAAGCAATAAAGCGATa                                              >  1:2193694/2‑48 (MQ=255)
                         aaGATTTGGTGCCTTATAAGATGTTCCGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAAcc                         >  1:2737387/2‑69 (MQ=255)
                         aaGATTTGGTGCCTTATAAGATGTTCCGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAAcc                         >  1:298350/2‑69 (MQ=255)
                         aaGATTTGGTGCCTTATAAGATGTTCCGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAAcc                         >  1:1842369/2‑69 (MQ=255)
                         aaGATTTGGTGCCTTATAAGATGTTCCGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAAc                          >  1:370574/2‑68 (MQ=255)
                              ttGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGgcgc                    >  1:2459959/1‑69 (MQ=255)
                                             aTGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     >  1:558927/1‑69 (MQ=255)
                                             aTGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     >  1:2550440/1‑69 (MQ=255)
                                             aTGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     >  1:2251240/1‑69 (MQ=255)
                                             aTGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     >  1:60552/1‑69 (MQ=255)
                                             aTGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     >  1:2179826/1‑69 (MQ=255)
                                             aTGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     >  1:1599941/1‑69 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:637438/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:902010/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:307051/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:2993824/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:2958202/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:2607605/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:2551495/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:1829107/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:1797997/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCGGCGCTGGTTTGc            <  1:1599714/57‑1 (MQ=255)
                                               gttccGTAGGAAGCAATAAAGCGATAACCTTCGATGAACTCCCAACCAGCGCTGGTTTGc            <  1:15644/57‑1 (MQ=255)
                                                tCCCGTAGGAAGCAATGAAGCGATAACCTTCGATTAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCAt  <  1:657398/69‑1 (MQ=255)
                                                          aGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     <  1:502965/56‑1 (MQ=255)
                                                          aGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     <  1:218826/56‑1 (MQ=255)
                                                          aGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     <  1:1337766/56‑1 (MQ=255)
                                                          aGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTc     <  1:1135569/56‑1 (MQ=255)
                                                                |                                                    
TTCCGTAGAAGCCATACAGTTGCCCCAGATTTGGTGCCTTATAAGATGTCCCGTAGGAAGCAATGAAGCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCAT  >  minE/2277470‑2277586

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A