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
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,742,822	A→G	71.2%	S400G (AGC→GGC)	ydhC →	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,742,822	0	A	G	71.2%	82.1 / 37.1	52	S400G (AGC→GGC)	ydhC	predicted transporter
Reads supporting (aligned to +/- strand): ref base A (4/11); new base G (21/16); total (25/27)
Fisher's exact test for biased strand distribution p-value = 6.85e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

TTACATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTTTGTTGTATGA  >  W3110S.gb/1742758‑1742887

ttACATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGa                                                               <  1:916745/69‑1 (MQ=255)

ttACATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCg                                                                <  1:1073490/68‑1 (MQ=255)

 tACATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGaa                                                              <  1:2220790/69‑1 (MQ=255)

  aCATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAAt                                                             <  1:804757/69‑1 (MQ=255)

   cATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAAt                                                             >  1:2994503/1‑68 (MQ=255)

     tgatgCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATca                                                           <  1:2023801/68‑1 (MQ=255)

          cAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTg                                                      <  1:584861/68‑1 (MQ=255)

            aCGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATc                                                   <  1:2871136/69‑1 (MQ=255)

            aCGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATc                                                   <  1:1787102/69‑1 (MQ=255)

            aCGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATc                                                   <  1:2190044/69‑1 (MQ=255)

             cGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATc                                                   <  1:2402433/68‑1 (MQ=255)

               ttGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCtat                                                <  1:3264331/69‑1 (MQ=255)

               ttGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCtat                                                <  1:3187784/69‑1 (MQ=255)

                    aagaagTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGa                                                               >  1:212763/1‑49 (MQ=255)

                      gaagTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATCTATATCGata                                         >  1:3585631/1‑69 (MQ=255)

                      gaagTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATCTATATCGata                                         >  1:1366021/1‑69 (MQ=255)

                          ttGGCTTCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGAtatact                                     <  1:59860/69‑1 (MQ=255)

                          ttGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATc                                                   >  1:939473/1‑55 (MQ=255)

                            ggCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCg                                                                <  1:2909936/40‑1 (MQ=255)

                              cTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATCTATATCGAtatacttat                                  <  1:80600/68‑1 (MQ=255)

                               tGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGAtatacttata                                 >  1:716850/1‑68 (MQ=255)

                               tGCCAGAATCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGAtatacttata                                 >  1:789485/1‑68 (MQ=255)

                                     aaTCATGGCAATGCCGAAGTCGCTCATGGCGAATca                                                           >  1:433930/1‑36 (MQ=255)

                                     aaTCATGGCAATGCCGAAGTCGCTCATGGCGAATca                                                           <  1:2548826/36‑1 (MQ=255)

                                     aaTCATGGCAATGCCGAAGTCGCTCATGGCGAATca                                                           >  1:839728/1‑36 (MQ=255)

                                     aaTCATGGCAATGCCGAAGTCGCTCATGGCGAATca                                                           <  1:593774/36‑1 (MQ=255)

                                      aTCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGgct                         >  1:1415230/1‑69 (MQ=255)

                                      aTCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGgct                         >  1:1640269/1‑69 (MQ=255)

                                      aTCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGgct                         >  1:3421817/1‑69 (MQ=255)

                                       tCATGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGgct                         >  1:1087157/1‑68 (MQ=255)

                                         aTGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATc                                                   >  1:2399470/1‑40 (MQ=255)

                                         aTGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATc                                                   >  1:2622542/1‑40 (MQ=255)

                                         aTGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGgctgct                      >  1:1536854/1‑69 (MQ=255)

                                         aTGGCAATGCCGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGgctgct                      >  1:870462/1‑69 (MQ=255)

                                                  ccGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAAt              >  1:244945/1‑68 (MQ=255)

                                                  ccGAAGTCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAAt              >  1:1811965/1‑68 (MQ=255)

                                                  ccGAAGTCGCTCATAGCGAATCACACTGATCTATATCGAtatact                                     >  1:3649368/1‑45 (MQ=255)

                                                    gAAGTCGCTCATAGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAAtttt           <  1:2608001/69‑1 (MQ=255)

                                                     aaGTCGCTCATAGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAAtttt           <  1:1373190/68‑1 (MQ=255)

                                                        tCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTttgttg       <  1:2026855/69‑1 (MQ=255)

                                                        tCGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTttgttg       >  1:825260/1‑69 (MQ=255)

                                                         cGCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTTtgttgt      <  1:2250381/69‑1 (MQ=255)

                                                          tcTCATAGCGAATCACACTGATCTATATCGAtatact                                     <  1:3100995/36‑1 (MQ=255)

                                                          gCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACaaaa               <  1:692175/59‑1 (MQ=255)

                                                          gCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACaaaa               <  1:2964640/59‑1 (MQ=255)

                                                          gCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTttgttg       >  1:3486960/1‑67 (MQ=255)

                                                          gCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTttgttg       >  1:3132535/1‑67 (MQ=255)

                                                          gCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTttgttg       >  1:302459/1‑67 (MQ=255)

                                                          gCTCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTTTGTTGTa     <  1:432612/69‑1 (MQ=255)

                                                          gCTCATAGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTttgttg       <  1:37232/67‑1 (MQ=255)

                                                            tCATGGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTTTGTTGTAt    <  1:2958040/68‑1 (MQ=255)

                                                             cATAGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTTTGTTGTATGa  >  1:2628976/1‑69 (MQ=255)

TTACATGATGCAACGTTGTGAAGAAGTTGGCTGCCAGAATCATGGCAATGCCGAAGTCGCTCATAGCGAATCACACTGATCTATATCGATATACTTATACTTAGGCTGCTAACAAAATTTTGTTGTATGA  >  W3110S.gb/1742758‑1742887

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