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
A3 F2 I1 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	Exported	609,726	G→C	23.5%	G176G (GGC→GGG)	pflB ←	pyruvate formate lyase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	609,726	0	G	C	23.5%	189.7 / 54.6	98	G176G (GGC→GGG)	pflB	pyruvate formate lyase I
Reads supporting (aligned to +/- strand): ref base G (51/24); new base C (10/13); total (61/37)
Fisher's exact test for biased strand distribution p-value = 4.86e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.98e-01

Only 100 of 114 total aligned reads displayed.

TGCCAGTTTGTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCG  >  Exported/609657‑609790

tgCCAGTTTGTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATacggc                                                                 >  1:274207/1‑71 (MQ=255)

   cAGTTTGTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATacggccac                                                              >  1:4086692/1‑71 (MQ=255)

   cAGTTTGTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATacggccac                                                              <  1:3335765/71‑1 (MQ=255)

        tGTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATacggccac                                                              >  1:3453361/1‑66 (MQ=255)

         gTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATAcggccacggcca                                                         <  1:4987662/70‑1 (MQ=255)

         gTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATAcggccacggcca                                                         >  1:4368058/1‑70 (MQ=255)

             ttCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCata                                                       >  1:572454/1‑68 (MQ=255)

              tcatcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGc                                                    <  1:2795615/70‑1 (MQ=255)

              tcatcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCa                                                   >  1:5208177/1‑71 (MQ=255)

                atcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                  <  1:739018/70‑1 (MQ=255)

                 tcaGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCt                                                <  1:5165410/71‑1 (MQ=255)

                        gTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGAc                                         <  1:1626945/71‑1 (MQ=255)

                         tCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGAc                                         <  1:5438625/70‑1 (MQ=255)

                          tgATGCCATACAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCg                                       >  1:4832129/2‑71 (MQ=255)

                           gATACCTTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCgg                                      >  1:2364034/1‑71 (MQ=255)

                           gATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATAcggccacggcca                                                         <  1:2112933/52‑1 (MQ=255)

                           gATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCgg                                      >  1:4304771/1‑71 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATacggccacggc                                                           >  1:3762709/1‑48 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                  >  1:2385760/1‑57 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                  >  1:5135949/1‑57 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                  >  1:2625745/1‑57 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                  >  1:867204/1‑57 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGt                                     >  1:1882342/1‑70 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGt                                     >  1:652340/1‑70 (MQ=255)

                             tACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGACACGGCCATATGCAt                                                  >  1:5125436/1‑57 (MQ=255)

                               ccatACAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATGTGGTAAACCGGTCAg                                  <  1:3584754/68‑1 (MQ=255)

                               ccatACAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAg                                  <  1:1652425/68‑1 (MQ=255)

                               ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCata                                                       <  1:1825870/50‑1 (MQ=255)

                               ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCata                                                       <  1:3301076/50‑1 (MQ=255)

                               ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAg                                  <  1:4882749/71‑1 (MQ=255)

                               ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAg                                  <  1:4061678/71‑1 (MQ=255)

                               ccGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAg                                  <  1:819147/71‑1 (MQ=255)

                                 gTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGaa                                >  1:1245798/1‑71 (MQ=255)

                                  tACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCa                                                   <  1:4261029/51‑1 (MQ=255)

                                  tACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGaa                                >  1:1790933/1‑70 (MQ=255)

                                   aCAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCa                                                   <  1:3353916/50‑1 (MQ=255)

                                    cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                             >  1:2959397/1‑54 (MQ=16)

                                    cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                             >  1:1897407/1‑54 (MQ=16)

                                    cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                             >  1:2969872/1‑54 (MQ=16)

                                    cAGCGCTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggt                                             >  1:2963213/1‑54 (MQ=16)

                                    cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCAt                                                  >  1:2296876/1‑50 (MQ=255)

                                    cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATc                                                 >  1:3114443/1‑51 (MQ=255)

                                    cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                             >  1:4111320/1‑71 (MQ=255)

                                    cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                             >  1:2925148/1‑71 (MQ=255)

                                    cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                             <  1:2323848/71‑1 (MQ=255)

                                    cAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                             >  1:3290189/1‑71 (MQ=255)

                                      gcgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                            <  1:111725/54‑3 (MQ=12)

                                       cgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                            <  1:1468219/53‑3 (MQ=12)

                                       cgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                            <  1:4648563/53‑3 (MQ=12)

                                       cgcTACGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTggta                                            <  1:1037542/53‑3 (MQ=12)

                                       cgcAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                             >  1:5112888/1‑68 (MQ=255)

                                       cgcAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAacac                             >  1:1550717/1‑68 (MQ=255)

                                        gctaCGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAg                          <  1:2540851/67‑1 (MQ=255)

                                        gctaCGCGGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGa                         <  1:3725503/68‑1 (MQ=255)

                                        gcAACGCGACGGTAGTCACCGATGATAcggccacggcca                                                         <  1:4342510/39‑1 (MQ=255)

                                        gcAACGCGACGGTAGTCACCGATGATAcggccacggcca                                                         <  1:4708354/39‑1 (MQ=255)

                                        gcAACGCGACGGTAGTCACCGATGATAcggccacggcca                                                         <  1:2937721/39‑1 (MQ=255)

                                          aaCGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGAtt                       <  1:2322149/71‑1 (MQ=255)

                                          aaCGCGACGGTAGTCACCGATGATACGGCCAAGGCCATATGCATCTGGAAGAc                                         >  1:3947898/1‑53 (MQ=39)

                                           aCGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGAtt                       >  1:343396/1‑70 (MQ=255)

                                            cgcgGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACGGGTCAGCACGCCAGAtt                       <  1:2976377/69‑1 (MQ=255)

                                            cgcgGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCa                                   >  1:2939260/1‑57 (MQ=12)

                                            cgcgGCGATAGTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTa                     >  1:1043154/1‑71 (MQ=255)

                                            cgcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                     >  1:1977826/1‑71 (MQ=255)

                                            cgcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                     <  1:3262171/71‑1 (MQ=255)

                                            cgcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                     <  1:4904901/71‑1 (MQ=255)

                                             gcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                     <  1:3497576/70‑1 (MQ=255)

                                             gcgACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGCTCAGAACACCAGATTTAc                    <  1:2408572/71‑1 (MQ=255)

                                                aCGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGc                 <  1:1593060/71‑1 (MQ=255)

                                                    tAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACg             >  1:3230450/1‑71 (MQ=255)

                                                     aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                               >  1:871138/1‑52 (MQ=255)

                                                     aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                               >  1:2650020/1‑52 (MQ=255)

                                                     aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                               >  1:4743364/1‑52 (MQ=255)

                                                     aGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAac                               >  1:4555955/1‑52 (MQ=255)

                                                      gTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACg             >  1:1429881/1‑69 (MQ=255)

                                                      gTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGAttt                      <  1:1618357/60‑1 (MQ=255)

                                                      gTCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGAttt                      <  1:267034/60‑1 (MQ=255)

                                                       tCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCa                           <  1:5566384/54‑1 (MQ=255)

                                                       tCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCa                           <  1:3137773/54‑1 (MQ=255)

                                                       tCACCGATAATGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAg          >  1:5050522/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACg                   >  1:5302453/1‑60 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACg                   >  1:4480444/1‑60 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:3952179/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:830147/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:3452840/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:1634714/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:5506485/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:1910296/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:5385352/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGa        >  1:2137121/1‑71 (MQ=255)

                                                         aCCGATGATACGGCCACGGCCATATGCATCTGGCAGACAGGTCAGAACACCAGATTTACGGCAACGCAgg         <  1:438047/70‑1 (MQ=255)

                                                           cGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATg      <  1:269486/71‑1 (MQ=255)

                                                            gatgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                     >  1:4793356/1‑55 (MQ=255)

                                                            gatgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTa                     >  1:2434345/1‑55 (MQ=255)

                                                            gatgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACg                   >  1:3314651/1‑57 (MQ=255)

                                                            gatgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACg                   >  1:2412064/1‑57 (MQ=255)

                                                            gataatGCGCCCACGGCCATAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCAtat     >  1:840490/1‑69 (MQ=255)

                                                             atgatACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTc    >  1:3351202/1‑71 (MQ=255)

                                                                atACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCg  >  1:5603563/1‑70 (MQ=255)

                                                                atACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCg  <  1:1230781/70‑1 (MQ=255)

TGCCAGTTTGTCTTTCATCAGGTAGTCGATACCGTACAGCGCAACGCGACGGTAGTCACCGATGATACGGCCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCG  >  Exported/609657‑609790

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