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
A5 F17 I0 R2	162	60.6	4616657	98.5%	4547407	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	345,099	C→T	17.5%	A155T (GCC→ACC)	yahN ←	neutral amino‑acid efflux system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	345,099	0	C	T	17.5%	95.2 / 13.0	40	A155T (GCC→ACC)	yahN	neutral amino‑acid efflux system
Reads supporting (aligned to +/- strand): ref base C (17/16); new base T (5/2); total (22/18)
Fisher's exact test for biased strand distribution p-value = 4.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

CGCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGTAAT  >  W3110S.gb/345032‑345165

cGCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTAtt                                                                 >  1:869408/1‑71 (MQ=255)

 gCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAttt                                                                <  1:1388831/71‑1 (MQ=255)

 gCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAtt                                                                 <  1:3124530/70‑1 (MQ=255)

   cAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTaa                                                              <  1:3258829/71‑1 (MQ=255)

      aTAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGt                                                           <  1:4581737/71‑1 (MQ=255)

        aaTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                         >  1:2288863/1‑71 (MQ=255)

         aTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTaa                                                              >  1:1875538/1‑65 (MQ=255)

         aTTGATGCGAGCACAATCCCCGCCCAGCCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTAc                                                        >  1:243109/1‑71 (MQ=255)

          ttGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATg                                                            <  1:2172757/66‑1 (MQ=255)

          ttGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACt                                                       <  1:2764373/71‑1 (MQ=255)

            gATGCGAGCACAATCCCAGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTa                                                               >  1:102197/1‑61 (MQ=255)

                      caATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACt                                            >  1:4268223/1‑70 (MQ=255)

                          ccccGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATa                                        >  1:918348/1‑70 (MQ=255)

                              gCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACt                                            <  1:3264549/62‑1 (MQ=255)

                              gCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTa                                                               >  1:108536/1‑43 (MQ=255)

                              gCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa                                                         >  1:2190343/1‑49 (MQ=255)

                               cccAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaa                                                  <  1:1888220/55‑1 (MQ=255)

                                ccAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATa                                 <  1:3950657/71‑1 (MQ=255)

                                 cAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaa                                <  1:2327164/71‑1 (MQ=255)

                                  aGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaa                                >  1:3366467/1‑70 (MQ=255)

                                   ggCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACTGAt                                         >  1:3723162/1‑60 (MQ=255)

                                    gCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAAc                             >  1:347622/1‑71 (MQ=255)

                                     ccATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACg                            <  1:328869/71‑1 (MQ=255)

                                       aTTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACt                                            >  1:3581760/1‑53 (MQ=255)

                                        ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTgag                                                    <  1:710651/44‑1 (MQ=255)

                                        ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGtt                         <  1:3596709/71‑1 (MQ=255)

                                          aaaCGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTgaga                                                   >  1:3573867/1‑43 (MQ=255)

                                          aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATa                                              >  1:4551807/1‑48 (MQ=255)

                                           aaCGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATa                                              >  1:1668086/1‑47 (MQ=255)

                                            aCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTga                                                     >  1:3798761/1‑39 (MQ=255)

                                                 cccATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGtt                 <  1:863949/70‑1 (MQ=255)

                                                   cATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga              <  1:3221137/71‑1 (MQ=255)

                                                   cATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga              <  1:1939953/71‑1 (MQ=255)

                                                       ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATa                                              >  1:3733553/1‑35 (MQ=255)

                                                       ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga              >  1:3788813/1‑67 (MQ=255)

                                                         ggTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGAt         <  1:2359851/70‑1 (MQ=255)

                                                         ggTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGAt         <  1:2580889/70‑1 (MQ=255)

                                                              ttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATc        >  1:2157992/1‑66 (MQ=255)

                                                               tCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGtaat  >  1:2737932/1‑71 (MQ=255)

                                                                cGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga              >  1:2974017/1‑58 (MQ=255)

CGCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGTAAT  >  W3110S.gb/345032‑345165

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A