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 1,605,808 T→C 20.6% H133H (CAT→CAC)  amiA → N‑acetylmuramoyl‑l‑alanine amidase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,605,8080TC20.6% 123.2 / 23.1 87H133H (CAT→CAC) amiAN‑acetylmuramoyl‑l‑alanine amidase I
Reads supporting (aligned to +/- strand):  ref base T (51/18);  new base C (11/7);  total (62/25)
Fisher's exact test for biased strand distribution p-value = 3.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.96e-01

TATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTGGGGCA  >  minE/1605742‑1605874
                                                                  |                                                                  
taacccACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg                                                                   >  1:2555619/4‑68 (MQ=255)
tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg                                                                   >  1:2070538/1‑68 (MQ=255)
tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg                                                                   >  1:2743256/1‑68 (MQ=255)
tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg                                                                   >  1:1290256/1‑68 (MQ=255)
tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg                                                                   >  1:482195/1‑68 (MQ=255)
tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg                                                                   >  1:475762/1‑68 (MQ=255)
  tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc                                                                 <  1:326306/68‑1 (MQ=255)
  tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc                                                                 <  1:1811357/68‑1 (MQ=255)
  tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc                                                                 <  1:453587/68‑1 (MQ=255)
  tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc                                                                 <  1:2054120/68‑1 (MQ=255)
  tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc                                                                 <  1:338006/68‑1 (MQ=255)
            cGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTa                                                       <  1:861832/68‑1 (MQ=255)
              aTCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTa                                                       <  1:200862/66‑1 (MQ=255)
                      gAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGaaa                                            >  1:318909/1‑69 (MQ=255)
                      gAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGaaa                                            >  1:3176543/1‑69 (MQ=255)
                      gAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGaaa                                            >  1:1997699/1‑69 (MQ=255)
                       aaaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:2681066/62‑1 (MQ=255)
                       aaaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:429010/62‑1 (MQ=255)
                       aaaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:1242439/62‑1 (MQ=255)
                       aaaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:2760816/62‑1 (MQ=255)
                       aaaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:3276798/62‑1 (MQ=255)
                       aaaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:223479/62‑1 (MQ=255)
                        aaTCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCACGCCGACGGTTTTACCAAc                                                  <  1:1737809/61‑1 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:3008078/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:2283325/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:284447/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:263846/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:2746564/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:3077431/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:2964791/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:364407/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:1911441/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:78794/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:1514579/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:46101/1‑69 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCt                                >  1:2244456/1‑68 (MQ=255)
                                   aaCATGGCGCAGATCTGTTTATGTCAATTCATACCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCtt                               >  1:3068604/1‑69 (MQ=255)
                                     cATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTTCCAACCCGAAAGCTGCCGGTGCTTc                              >  1:2227352/1‑68 (MQ=255)
                                     cATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTc                              >  1:2019128/1‑68 (MQ=255)
                                     cATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTc                              >  1:1101430/1‑68 (MQ=255)
                                     cATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTc                              >  1:2637484/1‑68 (MQ=255)
                                     cATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTc                              >  1:3221222/1‑68 (MQ=255)
                                     cATGGCGCAGATCTGTTTATGTCAATTCATCCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTc                              >  1:539958/1‑68 (MQ=255)
                                       tGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGt                           <  1:3178286/69‑1 (MQ=255)
                                       tGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGt                           <  1:1198488/69‑1 (MQ=255)
                                       tGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGt                           <  1:2397064/69‑1 (MQ=255)
                                       tGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGt                           <  1:2365550/69‑1 (MQ=255)
                                       tGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGt                           <  1:2007635/69‑1 (MQ=255)
                                            cAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTg                      >  1:128318/1‑69 (MQ=255)
                                              gATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGcc                    <  1:2933912/69‑1 (MQ=255)
                                              gATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGcc                    <  1:2968248/69‑1 (MQ=255)
                                              gATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGcc                    <  1:2314080/69‑1 (MQ=255)
                                              gATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGcc                    <  1:2252118/69‑1 (MQ=255)
                                              gATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGcc                    <  1:1841774/69‑1 (MQ=255)
                                              gATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGcc                    <  1:1037867/69‑1 (MQ=255)
                                                tCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCct                  >  1:1040309/1‑69 (MQ=255)
                                                 cTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCctc                 >  1:1403680/1‑69 (MQ=255)
                                                 cTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCctc                 >  1:2921279/1‑69 (MQ=255)
                                                    tttATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCctctct              >  1:2860403/1‑69 (MQ=255)
                                                      tATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTAtt                        >  1:1342544/1‑57 (MQ=255)
                                                      tATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTaa            >  1:1060100/1‑69 (MQ=255)
                                                      tATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTaa            >  1:531919/1‑69 (MQ=255)
                                                         gTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCg         >  1:3391623/1‑69 (MQ=255)
                                                         gTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCg         >  1:947057/1‑69 (MQ=255)
                                                         gTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCg         >  1:2057647/1‑69 (MQ=255)
                                                         gTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCg         >  1:2710003/1‑69 (MQ=255)
                                                         gTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCg         >  1:3198529/1‑69 (MQ=255)
                                                          tCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGt        >  1:1589749/1‑69 (MQ=255)
                                                          tCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGt        >  1:957865/1‑69 (MQ=255)
                                                          tCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGt        >  1:199097/1‑69 (MQ=255)
                                                          tCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGt        >  1:2292501/1‑69 (MQ=255)
                                                               tCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTggg     >  1:1770281/1‑67 (MQ=255)
                                                               tCATGCAGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTggg     >  1:1321/1‑67 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTa                          >  1:379128/1‑46 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:2606813/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:1042246/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:3087311/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:638321/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:3276675/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:255714/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:2566766/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:3240158/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:21834/1‑51 (MQ=255)
                                                               tCACGCCGACGGTTTTACAAACCCGAAAGCTGCCGGTGCTTCGGTATTTGc                     >  1:2838364/1‑51 (MQ=255)
                                                                cATGCCGATGTCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTGGGGCa  >  1:3377369/1‑69 (MQ=255)
                                                                cATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTGGGGCa  >  1:710660/1‑69 (MQ=255)
                                                                cATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTGGGGCa  >  1:1809942/1‑69 (MQ=255)
                                                                  |                                                                  
TATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCCGATGGCTTTACCAACCCGAAAGCTGCCGGTGCTTCGGTATTTGCCCTCTCTAACCGTGGGGCA  >  minE/1605742‑1605874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A