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 R2	230	93.6	4701257	96.3%	4527310	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,011,820	C→T	48.3%	R416R (CGC→CGT)	rstB →	sensory histidine kinase in two‑component regulatory system with RstA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,011,820	0	C	T	48.3%	11.1 / 121.6	89	R416R (CGC→CGT)	rstB	sensory histidine kinase in two‑component regulatory system with RstA
Reads supporting (aligned to +/- strand): ref base C (28/18); new base T (22/21); total (50/39)
Fisher's exact test for biased strand distribution p-value = 3.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCACGA  >  minE/1011751‑1011888

tGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCt                                                                     >  1:879254/1‑71 (MQ=255)

 gTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGttt                                                                    >  1:1589764/1‑71 (MQ=255)

        ctATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGtt                                                              >  1:2835948/1‑70 (MQ=255)

           taGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGc                                                          >  1:1186441/1‑71 (MQ=255)

             gCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTg                                                        >  1:361326/1‑71 (MQ=255)

             gCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTg                                                        >  1:2721600/1‑71 (MQ=255)

                  ggCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGt                                                   >  1:3909557/1‑71 (MQ=255)

                  ggCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGt                                                   >  1:718250/1‑71 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCg                                                    >  1:2618834/1‑69 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGt                                                   >  1:2139440/1‑70 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGt                                                   >  1:2720414/1‑70 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGt                                                   <  1:2716564/70‑1 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGt                                                   >  1:1584564/1‑70 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGt                                                   >  1:3287392/1‑70 (MQ=255)

                   gCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGt                                                   >  1:1699856/1‑70 (MQ=255)

                      aTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGttt                                                             <  1:2724962/57‑1 (MQ=255)

                      aTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTa                                                            <  1:1507435/58‑1 (MQ=255)

                      aTGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTa                                                            <  1:1321906/58‑1 (MQ=255)

                       tGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATgg                                              >  1:2649753/1‑71 (MQ=255)

                        gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATgg                                              >  1:2374939/1‑70 (MQ=255)

                        gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGc                                                          >  1:2181898/1‑58 (MQ=255)

                        gggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATg                                               >  1:40502/1‑69 (MQ=255)

                         ggCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGc                                             >  1:1329173/1‑70 (MQ=255)

                          gCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCAt                                           <  1:2995311/71‑1 (MQ=255)

                           cGGTACGGTTAATTGTGACACCACCGAACTGGGTGGTGCCCGCTTCTCGTTTa                                                            <  1:4395334/53‑1 (MQ=255)

                             gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                        <  1:1409168/71‑1 (MQ=255)

                             gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                        <  1:4293816/71‑1 (MQ=255)

                             gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTa                                                 <  1:1584177/62‑1 (MQ=255)

                             gTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAAc                                        <  1:151646/71‑1 (MQ=255)

                              tACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACa                                       <  1:3479672/71‑1 (MQ=255)

                              tACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCAt                                           <  1:220561/67‑1 (MQ=255)

                               aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACAt                                      >  1:670350/1‑71 (MQ=255)

                               aCGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTtctc                                                                 >  1:1149519/1‑44 (MQ=255)

                                cGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGt                                                   <  1:4364367/57‑1 (MQ=255)

                                cGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGtt                                                              >  1:1307147/1‑46 (MQ=255)

                                 ggTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATcc                                    <  1:4047723/71‑1 (MQ=255)

                                    tAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGt                                                   <  1:3900982/53‑1 (MQ=255)

                                    tAATTGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTa                                                 >  1:2391733/1‑55 (MQ=255)

                                      aTTGTGAGACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCa                                <  1:3356232/70‑1 (MQ=255)

                                       ttGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGc                                             <  1:303232/56‑1 (MQ=255)

                                       ttGTGACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAt                              >  1:1958366/1‑71 (MQ=255)

                                       ttGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATaa                                         <  1:2759060/60‑1 (MQ=255)

                                       ttGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTAAGGCATaa                                         <  1:2217871/60‑1 (MQ=255)

                                         gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACa                                       >  1:179167/1‑60 (MQ=255)

                                         gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCa                                <  1:800710/67‑1 (MQ=255)

                                         gtgACACCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCa                                <  1:2439810/67‑1 (MQ=255)

                                         gtgACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATccc                                   >  1:4060610/1‑64 (MQ=255)

                                          tgACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                           >  1:4668686/1‑71 (MQ=255)

                                            acacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTAcc                         >  1:1036722/1‑71 (MQ=255)

                                            acacCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTAcc                         <  1:3222849/71‑1 (MQ=255)

                                            acacCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTAc                          <  1:1260143/70‑1 (MQ=255)

                                             cacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTa                                                 >  1:998102/1‑46 (MQ=255)

                                             cacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACct                        <  1:3153878/71‑1 (MQ=255)

                                             cacCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACct                        <  1:1921415/71‑1 (MQ=255)

                                             cacCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTAt                                                >  1:317351/1‑47 (MQ=255)

                                             cacCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTAt                                                >  1:4148751/1‑47 (MQ=255)

                                              acCAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACctc                       >  1:1167449/1‑71 (MQ=255)

                                              acCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGc                                                          >  1:846317/1‑36 (MQ=255)

                                              acCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTAc                          >  1:3154004/1‑68 (MQ=255)

                                               ccAGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACa                                       <  1:999401/54‑1 (MQ=255)

                                                cAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCaa                               <  1:4280888/61‑1 (MQ=255)

                                                cAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTa                           >  1:4630784/1‑65 (MQ=255)

                                                cAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTAc                          >  1:3971528/1‑66 (MQ=255)

                                                cAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTg                     >  1:876631/1‑71 (MQ=255)

                                                cAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTg                     >  1:616954/1‑71 (MQ=255)

                                                 aGCGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                    <  1:3762294/71‑1 (MQ=255)

                                                 aGCGAACTGGGTGGTGCACGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGc                    >  1:1195777/1‑71 (MQ=255)

                                                   ggAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCt                  >  1:1041931/2‑71 (MQ=255)

                                                   cGAACTGGGTGGTGCCCGTTTCTCGTTTTGCTGGCCGt                                                   <  1:2281459/38‑1 (MQ=38)

                                                   cGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATc                                     <  1:2119492/52‑1 (MQ=255)

                                                   cGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCt                  >  1:4047222/1‑71 (MQ=255)

                                                   cGAACTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCt                  <  1:2759810/71‑1 (MQ=255)

                                                   cGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCa                                            <  1:2536941/45‑1 (MQ=255)

                                                   cGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCt                  <  1:4608511/71‑1 (MQ=255)

                                                   cGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCt                  <  1:199018/71‑1 (MQ=255)

                                                      aCTGGGTGGTGCCCGTTTCTCGTTTAGCTTGCCGTTATGGCATAAc                                        >  1:4093249/1‑46 (MQ=255)

                                                      aCTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGac               <  1:2942961/71‑1 (MQ=255)

                                                      aCTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTAACCTCTGc                    <  1:1337209/66‑1 (MQ=255)

                                                       cTGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGaca              >  1:3699697/1‑71 (MQ=255)

                                                        tGGGTGGTGCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCg                                  <  1:305670/50‑1 (MQ=255)

                                                        tGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATaa                                         >  1:3581080/1‑43 (MQ=255)

                                                        tGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATaa                                         >  1:3012612/1‑43 (MQ=255)

                                                          ggtggtGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTa           >  1:1130519/1‑71 (MQ=255)

                                                            tggtgCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTAcg         >  1:2570944/1‑71 (MQ=255)

                                                              gtgCCCGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCa                                <  1:775757/46‑1 (MQ=255)

                                                              gtgCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTAcgcg       <  1:474914/71‑1 (MQ=255)

                                                                gCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGcc                   >  1:1462320/1‑57 (MQ=255)

                                                                 cccGTTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCAc    >  1:2915673/1‑71 (MQ=255)

                                                                 cccGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCAc    >  1:2642375/1‑71 (MQ=255)

                                                                   cGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCACGa  >  1:4539383/1‑71 (MQ=255)

TGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATTTACCTCTGCCTGACACTACGCGCACGA  >  minE/1011751‑1011888

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