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 F3 I0 R2	232	76.3	4135488	90.9%	3759158	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,798,695	A→G	37.7%	Q239R (CAA→CGA)	proV →	glycine betaine transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,798,695	0	A	G	37.7%	49.4 / 66.8	61	Q239R (CAA→CGA)	proV	glycine betaine transporter subunit
Reads supporting (aligned to +/- strand): ref base A (20/18); new base G (11/12); total (31/30)
Fisher's exact test for biased strand distribution p-value = 7.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.74e-01

GCACCATTGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATGTCCG  >  minE/1798626‑1798764

gcACCATTGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCaa                                                                      <  1:2574989/71‑1 (MQ=255)

     aTTGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATgg                                                                 >  1:1119769/1‑71 (MQ=255)

      ttGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGt                                                                >  1:3822855/1‑71 (MQ=255)

      ttGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGt                                                                >  1:2925922/1‑71 (MQ=255)

      ttGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGt                                                                >  1:2391993/1‑71 (MQ=255)

        gTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTg                                                               <  1:3839602/70‑1 (MQ=255)

        gTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTg                                                               <  1:3043754/70‑1 (MQ=255)

        gTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTg                                                               <  1:3175036/70‑1 (MQ=255)

        gTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTg                                                               >  1:3209986/1‑70 (MQ=255)

        gTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTg                                                               <  1:2323083/70‑1 (MQ=255)

        gTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTg                                                               <  1:3578013/70‑1 (MQ=255)

        gTCTTTATTTCCCACGATCTTGAAGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTg                                                               <  1:542002/70‑1 (MQ=255)

         tCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGa                                                              <  1:2205607/70‑1 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:433658/1‑68 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:2624293/1‑68 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:2272803/1‑68 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:3956853/1‑68 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:3397636/1‑68 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:1568946/1‑68 (MQ=255)

             tATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAg                                                            >  1:835980/1‑68 (MQ=255)

              aTTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTGAAGTgg                                                         <  1:3684314/70‑1 (MQ=255)

                             gatgaAGCCATGCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTGAAGTGGTACAGGTCGGca                                             <  1:2966346/67‑1 (MQ=255)

                                   gCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGa                                   <  1:1723340/71‑1 (MQ=255)

                                   gCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGa                                   <  1:2944114/71‑1 (MQ=255)

                                       tGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAAtt                               <  1:1579275/71‑1 (MQ=255)

                                       tGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAAtt                               <  1:63166/71‑1 (MQ=255)

                                        gCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTGAAGTgg                                                         <  1:3030607/44‑1 (MQ=255)

                                        gCGTATTGGCGACCGAATTGCCATTATGCGAAATGGTGAAGTgg                                                         <  1:3093841/44‑1 (MQ=255)

                                         cGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATtct                             >  1:3810864/1‑71 (MQ=255)

                                         cGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATtct                             >  1:1323748/1‑71 (MQ=255)

                                         cGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATtct                             >  1:1132715/1‑71 (MQ=255)

                                          gTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATtct                             >  1:2535019/1‑70 (MQ=255)

                                           tATTGGCGACCGAATTGCCATTATGCAAAATGGTg                                                               <  1:955453/35‑1 (MQ=255)

                                             ttGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGaaa                                 >  1:2555851/1‑63 (MQ=255)

                                             ttGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGaaa                                 >  1:1991582/1‑63 (MQ=255)

                                             ttGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCaa                          <  1:3325108/70‑1 (MQ=255)

                                               ggCGACCGAATTGCCATTATGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCaataa                       >  1:339864/1‑71 (MQ=255)

                                               ggCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCaata                        <  1:3933412/70‑1 (MQ=255)

                                                gCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTGCAGGTCGGCACACCGGATGAAATTCTCaataa                       <  1:1204460/70‑1 (MQ=255)

                                                gCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCaataa                       <  1:1986731/70‑1 (MQ=255)

                                                gCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCaataa                       <  1:1982355/70‑1 (MQ=255)

                                                  gACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCaataat                      >  1:2884277/1‑69 (MQ=255)

                                                       aaTTGCCATTATGCGAAATTGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGa               <  1:238177/71‑1 (MQ=255)

                                                        aTTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGaa              >  1:1708158/1‑71 (MQ=255)

                                                        aTTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGaa              >  1:874873/1‑71 (MQ=255)

                                                         ttGCCATTATGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAAt             <  1:3559175/71‑1 (MQ=255)

                                                         ttGCCATTATGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAAt             <  1:369809/71‑1 (MQ=255)

                                                             cATTATGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGAtt         <  1:3856490/71‑1 (MQ=255)

                                                              aTTATGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTa        >  1:2341673/1‑71 (MQ=255)

                                                               ttATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAAtt                               <  1:545374/47‑1 (MQ=255)

                                                                 aTGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGa           >  1:3016873/1‑65 (MQ=255)

                                                                 aTGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGa           >  1:3865516/1‑65 (MQ=255)

                                                                 aTGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGa           >  1:3220603/1‑65 (MQ=255)

                                                                 aTGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGa           >  1:2182641/1‑65 (MQ=255)

                                                                 aTGCGAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATg      <  1:386021/70‑1 (MQ=255)

                                                                 aTGCAAAATGGTGAAGTGTTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATg            <  1:1174161/64‑1 (MQ=255)

                                                                 aTGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATg            <  1:1096281/64‑1 (MQ=255)

                                                                 aTGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATGt     >  1:3254768/1‑71 (MQ=255)

                                                                 aTGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATGt     >  1:1074315/1‑71 (MQ=255)

                                                                  tGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATg            <  1:3908437/63‑1 (MQ=255)

                                                                    cAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATGTcct  >  1:1124351/1‑70 (MQ=255)

                                                                    cAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATGTCCg  >  1:1275714/1‑71 (MQ=255)

GCACCATTGTCTTTATTTCCCACGATCTTGATGAAGCCATGCGTATTGGCGACCGAATTGCCATTATGCAAAATGGTGAAGTGGTACAGGTCGGCACACCGGATGAAATTCTCAATAATCCGGCGAATGATTATGTCCG  >  minE/1798626‑1798764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A