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 F17 I0 R1	67	74.8	3863507	93.7%	3620106	61.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,763,556	T→C	33.3%	noncoding (288/1542 nt)	rrsG ←	16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,763,556	0	T	C	33.3%	83.4 / 75.5	78	noncoding (288/1542 nt)	rrsG	16S ribosomal RNA
Reads supporting (aligned to +/- strand): ref base T (21/31); new base C (10/16); total (31/47)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

GGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCG  >  minE/1763502‑1763619

ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCtt                                                  <  1:3067370/70‑1 (MQ=31)

ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTg                                                 <  1:3580309/71‑1 (MQ=17)

ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTg                                                 <  1:1353910/71‑1 (MQ=17)

ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTg                                                 <  1:3614775/71‑1 (MQ=17)

 gAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTTCACCCTCTCAGGTCGGCTATGTATCGTCGCCTTgg                                                >  1:3581060/1‑71 (MQ=2)

 gAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTTCACCCTCTCAGGTCGGCTATGTATCGTCGCCTTg                                                 >  1:2235531/1‑70 (MQ=2)

 gAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCAGTTCACCCTCTCAGGTCGGCTATGTATCGTCGCCTTgg                                                >  1:601513/1‑71 (MQ=2)

  aGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTTCACCCTCTCAGGTCGGCTATGTATCGTCGCCTTGGt                                               <  1:1188356/71‑1 (MQ=2)

  aGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCCGTTCACCCTCTCAGGTCGGCTATGTATCGTCGCCTTGGt                                               <  1:2895331/71‑1 (MQ=2)

  aGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTg                                                 <  1:2001187/69‑1 (MQ=33)

  aGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGt                                               <  1:3280535/71‑1 (MQ=21)

        gACCGTGTCTCAGTTCCAGTGTGGCTGGTCGTCCTCTCAGACCAGCTACTGATCGTCGCCTTGGTGAGcc                                          <  1:1276022/70‑1 (MQ=11)

        gACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCg                                         <  1:1651276/71‑1 (MQ=21)

         aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                        <  1:3312568/71‑1 (MQ=34)

         aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                        >  1:2824007/1‑71 (MQ=34)

         aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                        <  1:419174/71‑1 (MQ=34)

         aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt                                        <  1:512421/71‑1 (MQ=34)

         aCCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAg                                            >  1:1720809/1‑67 (MQ=25)

          ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGtt                                       <  1:1353814/71‑1 (MQ=34)

            gtgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTAc                                     >  1:3244106/1‑71 (MQ=21)

             tgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcc                                    >  1:452679/1‑71 (MQ=34)

               tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:2689551/1‑70 (MQ=35)

               tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:170517/1‑70 (MQ=35)

               tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:2441173/1‑70 (MQ=35)

               tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:2436825/1‑70 (MQ=35)

               tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:150502/1‑70 (MQ=35)

                   aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc                               <  1:791606/70‑1 (MQ=25)

                   aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCccac                                <  1:2234261/69‑1 (MQ=25)

                   aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCccac                                <  1:739595/69‑1 (MQ=25)

                       ccAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTa                                      >  1:390862/1‑59 (MQ=35)

                       ccAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaaca                           <  1:2146004/70‑1 (MQ=255)

                       ccAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaaca                           <  1:1662966/70‑1 (MQ=255)

                       ccAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:3676075/1‑62 (MQ=25)

                       ccAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTAccc                                   >  1:2717576/1‑62 (MQ=25)

                        cAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAg                         <  1:304734/71‑1 (MQ=255)

                        cAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAg                         <  1:3473539/71‑1 (MQ=255)

                         aGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAg                         <  1:3695791/70‑1 (MQ=255)

                          gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGc                        >  1:3642117/1‑70 (MQ=255)

                          gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGc                        >  1:1141938/1‑70 (MQ=255)

                          gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt                       <  1:320928/71‑1 (MQ=255)

                          gtgtGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt                       <  1:3208442/71‑1 (MQ=255)

                           tgtgGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt                       >  1:340204/1‑70 (MQ=255)

                            gtgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa                     >  1:977931/1‑71 (MQ=255)

                            gtgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa                     >  1:2766787/1‑71 (MQ=255)

                            gtgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTa                      >  1:190083/1‑70 (MQ=255)

                             tgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAAt                    <  1:1026814/71‑1 (MQ=255)

                             tgGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAAt                    <  1:2446978/71‑1 (MQ=255)

                                 tGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaa                             <  1:2664534/58‑1 (MQ=255)

                                 tGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaa                             <  1:3361497/58‑1 (MQ=255)

                                 tGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaa                             <  1:2313754/58‑1 (MQ=255)

                                  ggTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCAt               >  1:2024931/1‑71 (MQ=255)

                                   gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCAt               <  1:2204171/70‑1 (MQ=255)

                                      aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGc                        >  1:2766034/1‑58 (MQ=255)

                                      aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGc                        >  1:3706355/1‑58 (MQ=255)

                                      aTCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCGCATCTgg           <  1:3137302/71‑1 (MQ=255)

                                      aTCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTgg           <  1:1753104/71‑1 (MQ=255)

                                      aTCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTgg           <  1:3806143/71‑1 (MQ=255)

                                       tCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTggg          <  1:3750461/71‑1 (MQ=255)

                                         ctctCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGca        >  1:3812875/1‑71 (MQ=255)

                                         ctctCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGca        >  1:1044599/1‑71 (MQ=255)

                                         ctctCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGc         <  1:1585343/70‑1 (MQ=255)

                                         ctctCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGc         <  1:828774/70‑1 (MQ=255)

                                         ctctCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa                     >  1:2590972/1‑58 (MQ=255)

                                         ctctCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa                     >  1:1418913/1‑58 (MQ=255)

                                         ctctAAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa                     >  1:1422271/1‑58 (MQ=17)

                                           ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccac                                >  1:2495309/1‑45 (MQ=38)

                                           ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt                       <  1:2585672/54‑1 (MQ=255)

                                           ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt                       <  1:1745853/54‑1 (MQ=255)

                                              aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGcaca      <  1:3410246/68‑1 (MQ=255)

                                              aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc   <  1:1986549/71‑1 (MQ=255)

                                              aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc   <  1:3666676/71‑1 (MQ=255)

                                              aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc   <  1:3654207/71‑1 (MQ=255)

                                              aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc   <  1:2210331/71‑1 (MQ=255)

                                              aGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc   <  1:390543/71‑1 (MQ=255)

                                              aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGGTAATCCCATCTGGGCACATcc   >  1:387983/1‑71 (MQ=255)

                                              aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGcaca      <  1:1187059/68‑1 (MQ=255)

                                               gACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCg  <  1:891453/71‑1 (MQ=255)

                                               gACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCg  <  1:2985554/71‑1 (MQ=255)

GGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCG  >  minE/1763502‑1763619

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