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 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,439,867	T→C	35.6%	intergenic (‑89/‑6)	nudC ← / → rsd	NADH pyrophosphatase/stationary phase protein, binds sigma 70 RNA polymerase subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,439,867	0	T	C	35.6%	69.0 / 74.5	73	intergenic (‑89/‑6)	nudC/rsd	NADH pyrophosphatase/stationary phase protein, binds sigma 70 RNA polymerase subunit
Reads supporting (aligned to +/- strand): ref base T (28/19); new base C (11/15); total (39/34)
Fisher's exact test for biased strand distribution p-value = 2.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATC  >  W3110S.gb/3439799‑3439933

aTCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCa                                                                  <  1:474109/71‑1 (MQ=255)

aTCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCa                                                                  <  1:4570221/71‑1 (MQ=255)

  cACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAAt                                                                >  1:653112/1‑71 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                <  1:2484489/70‑1 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                >  1:1270039/1‑70 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATc                                                               <  1:1308518/71‑1 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATc                                                               <  1:265000/71‑1 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATc                                                               <  1:4903909/71‑1 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATc                                                               <  1:367703/71‑1 (MQ=255)

   aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAAt                                                                >  1:2795199/1‑70 (MQ=255)

    cTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCa                                                              <  1:229265/71‑1 (MQ=255)

    cTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCa                                                              >  1:555302/1‑71 (MQ=255)

       gCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGc                                                           >  1:777949/1‑71 (MQ=255)

       gCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCAt                                                             <  1:2402178/69‑1 (MQ=255)

          tGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTa                                                        <  1:1542107/71‑1 (MQ=255)

          tGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTa                                                        <  1:3919178/71‑1 (MQ=255)

            tttAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAAt                                                                <  1:1431660/61‑1 (MQ=255)

            tttAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAAt                                                                <  1:531149/61‑1 (MQ=255)

             ttAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGc                                                           >  1:939390/1‑65 (MQ=255)

                   tGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                >  1:2719166/1‑54 (MQ=255)

                   tGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATc                                                               <  1:4154706/55‑1 (MQ=255)

                     gTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                              >  1:3958420/1‑70 (MQ=255)

                     gTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                              >  1:1420087/1‑70 (MQ=255)

                     gTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                              >  1:802472/1‑70 (MQ=255)

                     gTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                              >  1:4573597/1‑70 (MQ=255)

                       ttttACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATaa                                           >  1:3389334/1‑71 (MQ=255)

                       ttttACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAACTCGATaa                                           >  1:3999490/1‑71 (MQ=255)

                        tttACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCa                                                                  <  1:1395910/47‑1 (MQ=255)

                        tttACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCa                                                                  <  1:2670842/47‑1 (MQ=255)

                          tACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAAcc                                         >  1:76992/1‑70 (MQ=255)

                            cATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTg                                       >  1:3521607/1‑70 (MQ=255)

                            cATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGa                                      >  1:4585369/1‑71 (MQ=255)

                            cATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGa                                      <  1:4565029/71‑1 (MQ=255)

                            cATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGa                                      >  1:4846674/1‑71 (MQ=255)

                             aTTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGAc                                     <  1:4438171/71‑1 (MQ=255)

                              tttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCg                                               <  1:2803713/60‑1 (MQ=255)

                              tttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCg                                               <  1:406799/60‑1 (MQ=255)

                              tttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGGTAACCTGACg                                    <  1:1578299/71‑1 (MQ=255)

                               ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACg                                    >  1:4958929/1‑70 (MQ=255)

                               ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACg                                    >  1:2973201/1‑70 (MQ=255)

                               ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACg                                    >  1:2099983/1‑70 (MQ=255)

                                tctcACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACg                                    >  1:1237657/1‑69 (MQ=255)

                                  tcACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTc                                                <  1:2349685/55‑1 (MQ=255)

                                   cACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCa                                                                  <  1:4486310/36‑1 (MQ=255)

                                    aCTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGa                                              >  1:1929998/1‑55 (MQ=255)

                                    aCTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGa                                              >  1:4642623/1‑55 (MQ=255)

                                      tGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                            >  1:3195372/1‑71 (MQ=255)

                                      tGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                            >  1:3316843/1‑71 (MQ=255)

                                      tGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                            >  1:3128221/1‑71 (MQ=255)

                                      tGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                            >  1:2515654/1‑71 (MQ=255)

                                         gCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCag                         <  1:4975652/71‑1 (MQ=255)

                                             tttttGAATACAAACTTGCGGAGTCAATCATGCTTa                                                        <  1:4068737/36‑1 (MQ=255)

                                             tttttGAATACAAACTTGCGGAGCCAATCATGCTTa                                                        <  1:3816393/36‑1 (MQ=255)

                                             tttttGAATACAAACTTGCGGAGCCAATCATGCTTa                                                        <  1:1219651/36‑1 (MQ=255)

                                             tttttGAATACAAACTTGCGGAGCCAATCATGCTTa                                                        <  1:3165748/36‑1 (MQ=255)

                                             tttttGAATACAAACTTGCGGAGCCAATCATGCTTa                                                        <  1:789838/36‑1 (MQ=255)

                                             tttttGAATACAAACTTGCGGAGCCAATCATGCTTa                                                        <  1:4862624/36‑1 (MQ=255)

                                             tttctGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTc                           <  1:5072235/65‑1 (MQ=255)

                                              ttttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATa                                            <  1:2291218/47‑1 (MQ=255)

                                              ttttGAATACAAACTTGCGGAGCCAATCATGCTTAAc                                                      >  1:4212510/1‑37 (MQ=255)

                                               tttGAATACAAACTTGCGGAGTCAATCATGCTTaa                                                       >  1:2058327/1‑35 (MQ=255)

                                               tttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAg                   >  1:525141/1‑71 (MQ=255)

                                               tttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAg                   >  1:3725801/1‑71 (MQ=255)

                                               tttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAg                   >  1:2850528/1‑71 (MQ=255)

                                                    aTACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACa              <  1:4205547/71‑1 (MQ=255)

                                                     tACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACaa             <  1:1278358/71‑1 (MQ=255)

                                                       cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACg                                    >  1:2513516/1‑46 (MQ=255)

                                                       cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAg                                 >  1:3525043/1‑49 (MQ=255)

                                                       cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAg                                 >  1:1858755/1‑49 (MQ=255)

                                                       cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAAc           >  1:4489748/1‑71 (MQ=255)

                                                       cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAAc           >  1:4090777/1‑71 (MQ=255)

                                                          aCTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTgg        >  1:2820948/1‑71 (MQ=255)

                                                           cTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGt       >  1:4344336/1‑71 (MQ=255)

                                                                    tCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATc  <  1:997571/67‑1 (MQ=255)

ATCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATC  >  W3110S.gb/3439799‑3439933

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