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	1,966,797	T→C	40.9%	V611V (GTA→GTG)	tktA ←	transketolase 1, thiamin‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,966,797	0	T	C	40.9%	38.8 / 76.8	105	V611V (GTA→GTG)	tktA	transketolase 1, thiamin‑binding
Reads supporting (aligned to +/- strand): ref base T (46/16); new base C (22/21); total (68/37)
Fisher's exact test for biased strand distribution p-value = 2.20e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

Only 100 of 105 total aligned reads displayed.

CGATAGCACCGTTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCA  >  minE/1966742‑1966863

cgaTAGCACCGTTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTg                                                       <  1:2050901/69‑1 (MQ=255)

cgaTAGCACCGTTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTg                                                       <  1:2405162/69‑1 (MQ=255)

cgaTAGCACCGTTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTg                                                       <  1:1750765/69‑1 (MQ=255)

cgaTAGCACCGTTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTg                                                       <  1:1746953/69‑1 (MQ=255)

           ttCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCt                                            <  1:3360125/69‑1 (MQ=255)

                        aCTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACgg                               <  1:2683651/69‑1 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACgg                               >  1:377830/1‑68 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                              >  1:537404/1‑69 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                              >  1:801063/1‑69 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                              >  1:2338927/1‑69 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                              >  1:2969400/1‑69 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                              >  1:2753760/1‑69 (MQ=255)

                         cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                              >  1:1508768/1‑69 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:931623/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:1885040/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:1541850/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:273258/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:277648/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:616966/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                >  1:3358979/1‑55 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCTCGGTAagc                  >  1:2917857/1‑69 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  >  1:1550914/1‑69 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  <  1:2614879/69‑1 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  >  1:2881214/1‑69 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  <  1:141516/69‑1 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  <  1:2414322/69‑1 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  >  1:846259/1‑69 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  <  1:2260922/69‑1 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  <  1:355885/69‑1 (MQ=255)

                                     gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                  <  1:1116979/69‑1 (MQ=255)

                                          cAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAgcagca              <  1:548111/68‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:200444/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:1135545/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:557757/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:344441/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:126422/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:3324875/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:3182777/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:3113316/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:3060681/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:3038477/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:302468/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:1290308/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:1372726/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:2825118/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:1101994/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:912374/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:221076/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:2399533/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:1855013/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:2194653/58‑1 (MQ=255)

                                           aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                       <  1:2175773/58‑1 (MQ=255)

                                            aTACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATcc           >  1:2490924/1‑69 (MQ=255)

                                            aTACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATcc           >  1:2072594/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTa                                  >  1:2730152/1‑43 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGAtt                            >  1:2869574/1‑49 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTg         >  1:2080867/1‑68 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTg         >  1:1454706/1‑68 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:3333983/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:2400430/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:3107019/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:1271673/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:845724/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:2356833/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:1192939/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:2916187/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:1188079/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:1815986/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:888251/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:145970/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:714199/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:2642203/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:1732384/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:1982753/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:2590009/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc        >  1:2561034/1‑69 (MQ=255)

                                               cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGAATCACGGTAAGCAGCATCCTGc        >  1:337571/1‑69 (MQ=255)

                                               cccGCTTCTACAACAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAACATCCTGc        >  1:1476233/1‑69 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCCCGGTAagccgcg              >  1:1243044/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:77829/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:94475/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:68858/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:706339/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:726337/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:769279/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:361510/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:3065635/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:2965961/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:2671674/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:2597659/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:2565933/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:1980205/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:1854725/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:184328/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:1807444/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:1477895/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg              >  1:1455748/1‑59 (MQ=255)

                                                  gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACAGTAagccgcg              >  1:1516350/1‑59 (MQ=255)

                                                     tCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCa  <  1:2871655/69‑1 (MQ=255)

                                                     tCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCa  <  1:195973/69‑1 (MQ=255)

CGATAGCACCGTTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCA  >  minE/1966742‑1966863

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