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
A6 F21 I0 R2	370	72.1	3738297	91.5%	3420541	62.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	826,223	G→T	56.9%	G207V (GGT→GTT)	ychP →	predicted invasin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	826,223	0	G	T	56.9%	‑3.6 / 105.1	72	G207V (GGT→GTT)	ychP	predicted invasin
Reads supporting (aligned to +/- strand): ref base G (13/18); new base T (13/28); total (26/46)
Fisher's exact test for biased strand distribution p-value = 4.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGCTCGGATGCGCATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGTCTGGGATTAAAT  >  minE/826157‑826293

cAGCTCGGATGCGCATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGAt                                                                    >  1:1839743/1‑71 (MQ=255)

   cTCGGATGCGCATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCgt                                                                 <  1:2400302/71‑1 (MQ=255)

   cTCGGATGCGCATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCgt                                                                 <  1:1350874/71‑1 (MQ=255)

   cTCGGATGCGCATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCgt                                                                 <  1:911900/71‑1 (MQ=255)

           cgcATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTg                                                             <  1:1095257/67‑1 (MQ=255)

           cgcATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGAtt                                                          <  1:1799178/70‑1 (MQ=255)

            gcATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTg                                                        <  1:663098/71‑1 (MQ=255)

             cATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGt                                                       <  1:1620360/71‑1 (MQ=255)

               tGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGttt                                                     <  1:2454843/71‑1 (MQ=255)

               tGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGttt                                                     <  1:3214566/71‑1 (MQ=255)

                gCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGttt                                                     >  1:736749/1‑70 (MQ=255)

                 ccGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGAt                                                                    >  1:1936719/1‑54 (MQ=255)

                  cGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAAc                                                  >  1:150425/1‑71 (MQ=255)

                    ttCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCg                                                                  <  1:1520176/53‑1 (MQ=255)

                      cTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTg                                              >  1:2597099/1‑71 (MQ=255)

                       tATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTgg                                             >  1:2393662/1‑71 (MQ=255)

                           aaCACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACg                                         <  1:2112253/71‑1 (MQ=255)

                            acacCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTAc                                          <  1:562181/69‑1 (MQ=255)

                            acacCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACgg                                        >  1:865655/1‑71 (MQ=255)

                             cacCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTg                                              <  1:1704701/64‑1 (MQ=255)

                             cacCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTg                                              <  1:2710076/64‑1 (MQ=255)

                             cacCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACggg                                       >  1:722038/1‑71 (MQ=255)

                              acCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGAtt                                                          <  1:1501855/51‑1 (MQ=255)

                              acCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGAtt                                                          <  1:3182111/51‑1 (MQ=255)

                              acCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGAtt                                                          <  1:2850741/51‑1 (MQ=255)

                              acCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGAtt                                                          <  1:286894/51‑1 (MQ=255)

                              acCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGAtt                                                          <  1:2962771/51‑1 (MQ=255)

                               ccTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTggc                                            >  1:1038031/1‑63 (MQ=255)

                               ccTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTggc                                            >  1:198580/1‑63 (MQ=255)

                               ccTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGtt                                     <  1:1303726/71‑1 (MQ=255)

                                cTCAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTa                                    <  1:847130/71‑1 (MQ=255)

                                cTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCgt                                                                 <  1:311114/42‑1 (MQ=255)

                                cTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTa                                    <  1:3217867/71‑1 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGAtt                                                          <  1:300833/47‑1 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTgg                                             <  1:2294885/60‑1 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTgg                                             <  1:2773386/60‑1 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   >  1:2055591/1‑70 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   >  1:1686321/1‑70 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   >  1:1142326/1‑70 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   >  1:1138046/1‑70 (MQ=255)

                                  cAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   >  1:1056419/1‑70 (MQ=255)

                                   aaTACCAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATca                                 >  1:3536811/1‑71 (MQ=255)

                                   aaTACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   <  1:1275176/69‑1 (MQ=255)

                                    aTACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTAt                                   <  1:1041485/68‑1 (MQ=255)

                                        cAGTGTCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATc                            <  1:359918/71‑1 (MQ=255)

                                          gtgtCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATccc                          <  1:1354377/71‑1 (MQ=255)

                                           tgtCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCg                         <  1:3295287/71‑1 (MQ=255)

                                            gtCAGCCTAGAACAGTATTTTGTTGATCGTGTTGAttt                                                         <  1:2888568/38‑1 (MQ=255)

                                             tCAGCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTc                       >  1:171938/1‑71 (MQ=255)

                                               aGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTAc                                          >  1:2364249/1‑50 (MQ=255)

                                               aGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTcgc                     <  1:3660918/71‑1 (MQ=255)

                                               aGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTcgc                     <  1:3656626/71‑1 (MQ=255)

                                                gCCTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTc                       <  1:14913/68‑1 (MQ=255)

                                                  cTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACgg                                        >  1:3199773/1‑49 (MQ=255)

                                                  cTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCg                         >  1:2832888/1‑64 (MQ=255)

                                                  cTAGAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTcgc                     >  1:1427917/1‑68 (MQ=255)

                                                   tAGAACAGTATTTTGGTGATCGTGTTGATTTGttt                                                     <  1:1600143/35‑1 (MQ=255)

                                                   tAGAACAGTATTTTGGTGATCGTGTTGATTTGttt                                                     <  1:388564/35‑1 (MQ=255)

                                                   tAGAACAGTATTTTGGTGATCGTGTTGATTTGttt                                                     <  1:2875102/35‑1 (MQ=255)

                                                   tAGAACAGTATTTTGGTGATCGTGTTGATTTGttt                                                     <  1:384225/35‑1 (MQ=255)

                                                     gAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTg                 <  1:2643103/69‑1 (MQ=255)

                                                     gAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGa                <  1:290039/70‑1 (MQ=255)

                                                     gAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGa                <  1:2957860/70‑1 (MQ=255)

                                                     gAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAg               <  1:1666655/71‑1 (MQ=255)

                                                     gAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAg               <  1:664817/71‑1 (MQ=255)

                                                     gAACAGTATTTTGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAg               <  1:98084/71‑1 (MQ=255)

                                                        cAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGTCt            <  1:217321/71‑1 (MQ=255)

                                                          gTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGTCTgg          >  1:2229841/1‑71 (MQ=255)

                                                             ttttGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATcac                                >  1:3515037/1‑46 (MQ=255)

                                                             ttttGTTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATcac                                >  1:1705583/1‑46 (MQ=255)

                                                               ttGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGt              >  1:467388/1‑62 (MQ=255)

                                                               ttGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGTCTGGGAt       >  1:3128926/1‑69 (MQ=255)

                                                                  gTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGTCTGGGATTAAAt  <  1:1348620/71‑1 (MQ=255)

CAGCTCGGATGCGCATGCCGTTCTATCAACACCTCAATACCAGTGTCAGCCTAGAACAGTATTTTGGTGATCGTGTTGATTTGTTTAACTCTGGTACGGGTTATCACAATCCCGTCGCGTTGAGTCTGGGATTAAAT  >  minE/826157‑826293

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