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	677,935	G→A	48.7%	L33L (CTG→CTA)	yccR →	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	677,935	0	G	A	48.7%	10.3 / 146.2	160	L33L (CTG→CTA)	yccR	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (47/35); new base A (17/61); total (64/96)
Fisher's exact test for biased strand distribution p-value = 5.19e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01

Only 100 of 162 total aligned reads displayed.

AATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCAA  >  minE/677868‑678001

aaTCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTg                                                                    <  1:3150081/68‑1 (MQ=255)

aaTCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTg                                                                    <  1:3171062/68‑1 (MQ=255)

  tCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGAcc                                                                 <  1:118037/69‑1 (MQ=255)

  tCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGAcc                                                                 <  1:3289989/69‑1 (MQ=255)

    acaAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCg                                                                >  1:1047887/1‑68 (MQ=255)

         aaTACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGtt                                                              <  1:2357204/65‑1 (MQ=255)

           tACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTgacgac                                                        <  1:2580633/69‑1 (MQ=255)

             ccTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                                      >  1:2209405/1‑69 (MQ=255)

             ccTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                                      >  1:1235563/1‑69 (MQ=255)

             catGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGacac                                                      >  1:2826625/3‑69 (MQ=255)

                 gCAACGTTGGTCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:937566/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:484241/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:43917/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:1351293/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:2139204/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:2341856/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:243331/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:3224569/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:1173402/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:2467437/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:1060332/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:289027/1‑69 (MQ=255)

                 gCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGgtg                                                  >  1:767130/1‑69 (MQ=255)

                         gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                                          <  1:1247838/69‑1 (MQ=255)

                         gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                                          >  1:2021383/1‑69 (MQ=255)

                         gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                                          <  1:2207475/69‑1 (MQ=255)

                         gggCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                                          >  1:641243/1‑69 (MQ=255)

                         gggAACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGAt                                          >  1:3135723/1‑69 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:2613474/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:2496590/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:751498/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:92382/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:3376391/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:1017327/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:3425544/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:373572/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:552852/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:2104386/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:1617559/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:2042723/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:1357395/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:1191369/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:1051599/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGTAGTTACAGCCTAACCGTTg                                                             <  1:1088962/40‑1 (MQ=255)

                                   gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGa                                 >  1:836989/1‑68 (MQ=255)

                                   gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGa                                 >  1:1650798/1‑68 (MQ=255)

                                   gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGAt                                >  1:2412156/1‑69 (MQ=255)

                                   gAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGAt                                >  1:1855575/1‑69 (MQ=255)

                                             cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:3334038/69‑1 (MQ=255)

                                             cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:2618209/69‑1 (MQ=255)

                                             cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:804239/69‑1 (MQ=255)

                                             cATTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGATGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:3123514/69‑1 (MQ=255)

                                             cATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:1979010/69‑1 (MQ=255)

                                             cATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:2623667/69‑1 (MQ=255)

                                              aTTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:3017154/68‑1 (MQ=255)

                                              aTTGTTTGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGt                      <  1:1000490/68‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:3063862/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:2981321/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:2932008/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:1389736/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:1385604/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:1075867/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:1815232/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:910043/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:226217/45‑1 (MQ=255)

                                                   ttGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:2136856/45‑1 (MQ=255)

                                                    tGGTAGTTACAGCCTAACCGTTGACGACACGGTGTTTGCGATgg                                        <  1:96072/44‑1 (MQ=38)

                                                         gTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:3048008/1‑69 (MQ=255)

                                                         gTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:275828/1‑69 (MQ=255)

                                                         gTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:2591976/1‑69 (MQ=255)

                                                         gTTACAGCCTGACCGTTGACGACACCGTGTTTGCGATGCTTTCTGATGGTGAGTTGTATCTTCGAGc            >  1:1731941/1‑67 (MQ=255)

                                                           tACAGCCTGACCGTTGACGCCACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:1543216/1‑67 (MQ=255)

                                                           tACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:2013975/1‑67 (MQ=255)

                                                           tACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:1513421/1‑67 (MQ=255)

                                                           tACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:2515466/1‑67 (MQ=255)

                                                           tACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCtt          >  1:2667089/1‑67 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     <  1:1620084/55‑1 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:2001856/1‑55 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:1938821/1‑55 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:2441114/1‑55 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:559105/1‑55 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     <  1:1294541/55‑1 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     <  1:1690399/55‑1 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     <  1:3413540/55‑1 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     <  1:2884150/55‑1 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:3344050/1‑55 (MQ=255)

                                                            aCAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:1426734/1‑55 (MQ=255)

                                                            aCAGCCAGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTa                     >  1:511216/1‑55 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:269366/69‑1 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:2925469/69‑1 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:2805884/69‑1 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:1552405/69‑1 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:343416/69‑1 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:492426/69‑1 (MQ=255)

                                                                ccTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:264672/69‑1 (MQ=255)

                                                                 cTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCaa  >  1:3250783/1‑69 (MQ=255)

                                                                 cTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCaa  >  1:1846533/1‑69 (MQ=255)

                                                                 cTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCaa  >  1:1944900/1‑69 (MQ=255)

                                                                 cTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCa   <  1:1215396/68‑1 (MQ=255)

                                                                  tGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCaa  <  1:1292139/68‑1 (MQ=255)

AATCACAAGAATACCTGGCAACGTTGGGCACAATTGAATACCGATCATTGTTTGGCAGTTACAGCCTGACCGTTGACGACACGGTGTTTGCGATGGTTTCTGATGGTGAGTTGTATCTTCGGGCTTGTGAGCAA  >  minE/677868‑678001

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