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	3,439,867	T→C	10.9%	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	10.9%	246.3 / 19.7	92	intergenic (‑89/‑6)	nudC/rsd	NADH pyrophosphatase/stationary phase protein, binds sigma 70 RNA polymerase subunit
Reads supporting (aligned to +/- strand): ref base T (41/41); new base C (7/3); total (48/44)
Fisher's exact test for biased strand distribution p-value = 3.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

CATCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATCGCTG  >  W3110S.gb/3439798‑3439937

cATCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTc                                                                       <  1:2525000/71‑1 (MQ=255)

    aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                    <  1:767467/70‑1 (MQ=255)

    aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                    >  1:1790730/1‑70 (MQ=255)

    aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                    >  1:290238/1‑70 (MQ=255)

    aCTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAAt                                                                    <  1:1131922/70‑1 (MQ=255)

     cTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCa                                                                  >  1:2698075/1‑71 (MQ=255)

       ggCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATg                                                                >  1:2760631/1‑71 (MQ=255)

        gCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGc                                                               >  1:2272745/1‑71 (MQ=255)

          aTGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCtt                                                             <  1:1611815/71‑1 (MQ=255)

          aTGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCtt                                                             <  1:2055315/71‑1 (MQ=255)

           tGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTa                                                            <  1:4139190/71‑1 (MQ=255)

             tttAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCtt                                                             <  1:4343895/68‑1 (MQ=255)

              ttAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAAc                                                          >  1:3768790/1‑70 (MQ=255)

              ttAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAAc                                                          >  1:2911449/1‑70 (MQ=255)

               tAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAAc                                                          >  1:4403507/1‑69 (MQ=255)

                aaCATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAg                                                       >  1:1929173/1‑71 (MQ=255)

                  cATGGTTTTTACATTTCTCACTGAGCATTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCt                                                     <  1:4365468/71‑1 (MQ=255)

                    tGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCg                                                   <  1:4572790/71‑1 (MQ=255)

                     ggTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGATTCAATCATg                                                                <  1:1014174/57‑1 (MQ=255)

                     ggTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                                  >  1:1017175/1‑71 (MQ=255)

                     ggTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                                  >  1:1011568/1‑71 (MQ=255)

                      gTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGa                                                  >  1:1935846/1‑70 (MQ=255)

                        ttttACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATa                                                >  1:2172064/1‑70 (MQ=255)

                            aCATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCt                                            >  1:4330360/1‑70 (MQ=255)

                            aCATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCt                                            <  1:1771733/70‑1 (MQ=255)

                             cATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGa                                          >  1:3239669/1‑71 (MQ=255)

                                ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTaa                                                           >  1:4183637/1‑51 (MQ=255)

                                ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACg                                        >  1:3776873/1‑70 (MQ=255)

                                ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTGACCAGCTCGATAACCTGACg                                        >  1:4460298/1‑70 (MQ=255)

                                ttCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACg                                        >  1:452824/1‑70 (MQ=255)

                                  ctcACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGa                                      <  1:1662333/70‑1 (MQ=255)

                                   tcACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATc                                                                   <  1:2321517/40‑1 (MQ=255)

                                   tcACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTc                                                    >  1:3845268/1‑55 (MQ=255)

                                     aCTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCCATAACCTGACGGAgc                                    <  1:4247618/69‑1 (MQ=255)

                                         aGCAGTTTTTGAATACAAACTTGCTGAGTCAATCATGc                                                               >  1:2816918/1‑38 (MQ=255)

                                         aGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGc                                                               >  1:2985504/1‑38 (MQ=255)

                                         aGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                                >  1:534065/1‑69 (MQ=255)

                                         aGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                                >  1:4065212/1‑69 (MQ=255)

                                         aGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                                >  1:4059752/1‑69 (MQ=255)

                                          gCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCag                             <  1:1458507/71‑1 (MQ=255)

                                           cAGTTTTTGAATACAAACTTGCTGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCaga                            <  1:4132074/71‑1 (MQ=255)

                                           cAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCaga                            <  1:2755259/71‑1 (MQ=255)

                                           cAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCa                              <  1:1197383/69‑1 (MQ=255)

                                           cAGTTTTTGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCaga                            <  1:4586835/71‑1 (MQ=255)

                                            aGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCagag                           <  1:2082864/71‑1 (MQ=255)

                                             gTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCagag                           >  1:2527526/1‑70 (MQ=255)

                                             gTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCagag                           >  1:3528141/1‑70 (MQ=255)

                                             gTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAgg                          <  1:1298867/71‑1 (MQ=255)

                                             gTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAgg                          <  1:3473443/71‑1 (MQ=255)

                                             gTTTTTGAATACAAACTTGCGGAGTCAATAATGCTTAACCAGCTCGATAACCTGACGGa                                      >  1:983769/1‑59 (MQ=255)

                                              tttttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCg                                                   <  1:417475/45‑1 (MQ=255)

                                              tttttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCa                              <  1:3406011/66‑1 (MQ=255)

                                               ttttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAAc                                              >  1:2495559/1‑49 (MQ=255)

                                               ttttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAAc                                              >  1:3242835/1‑49 (MQ=255)

                                               ttttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAgg                          >  1:3257063/1‑69 (MQ=255)

                                                tttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCt                                                     >  1:3905592/1‑41 (MQ=255)

                                                tttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAg                       >  1:2100061/1‑71 (MQ=255)

                                                tttGAATACAAACTTGCGGAGTCAATCATCCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGaa                        <  1:1222438/70‑1 (MQ=255)

                                                tttGAATACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAg                       >  1:819699/1‑71 (MQ=255)

                                                 ttGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAg                       <  1:1486630/70‑1 (MQ=255)

                                                  tGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGt                      >  1:3042367/1‑70 (MQ=255)

                                                  tGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGt                      <  1:3943753/70‑1 (MQ=255)

                                                   gAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTa                     <  1:1584571/70‑1 (MQ=255)

                                                    aaTACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATa                                                <  1:2110344/42‑1 (MQ=255)

                                                    aaTACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAgg                          <  1:3803481/64‑1 (MQ=255)

                                                     aTACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAAc                   >  1:2406545/1‑70 (MQ=255)

                                                     aTACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACa                  <  1:1362761/71‑1 (MQ=255)

                                                      tACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACaa                 <  1:2541213/71‑1 (MQ=255)

                                                      tACAAACTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGt                      <  1:3473090/66‑1 (MQ=255)

                                                       aCAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCt                                            <  1:2654895/43‑1 (MQ=255)

                                                        cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGa                         >  1:4360828/1‑61 (MQ=255)

                                                        cAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACaaa                <  1:1916184/70‑1 (MQ=255)

                                                         aaaCTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAg                                     >  1:2007508/1‑48 (MQ=255)

                                                         aaaCTTGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACt              >  1:148065/1‑71 (MQ=255)

                                                          aaCTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTg             >  1:525253/1‑71 (MQ=255)

                                                           aCTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCa                              <  1:1184382/53‑1 (MQ=255)

                                                             ttGCGGATTCAATCATGCTTAACCAGCTCGATAACCTGACGGAg                                     >  1:3267003/1‑44 (MQ=255)

                                                             ttGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGtt          >  1:891501/1‑71 (MQ=255)

                                                             ttGCGGAGCCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGt                                >  1:4553746/1‑49 (MQ=255)

                                                               gCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTg         <  1:3183555/70‑1 (MQ=255)

                                                               gCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGa        >  1:1914736/1‑71 (MQ=255)

                                                               gCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGa        >  1:2972318/1‑71 (MQ=255)

                                                                cGGAGTCAATCATGCTTAACCAGCTCGATACCCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGAt       <  1:3559481/71‑1 (MQ=255)

                                                                cGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTgc        <  1:2049921/70‑2 (MQ=255)

                                                                 ggAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTg         <  1:2312892/68‑1 (MQ=255)

                                                                 ggAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTg         <  1:2307357/68‑1 (MQ=255)

                                                                  gAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGa        <  1:1401899/68‑1 (MQ=255)

                                                                  gAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATCg     <  1:3033202/71‑1 (MQ=255)

                                                                   aGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTg             >  1:1894691/1‑62 (MQ=255)

                                                                   aGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATCGc    >  1:4181644/1‑71 (MQ=255)

                                                                    gTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGcgcg                                 >  1:2683525/1‑41 (MQ=255)

                                                                    gTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGa        <  1:4417508/66‑1 (MQ=255)

                                                                     tCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAgg                          <  1:4123064/47‑1 (MQ=255)

                                                                     tCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATCGCTg  >  1:1360595/1‑71 (MQ=255)

CATCACTGGCATGTTTAACATGGTTTTTACATTTCTCACTGAGCAGTTTTTGAATACAAACTTGCGGAGTCAATCATGCTTAACCAGCTCGATAACCTGACGGAGCGCGTCAGAGGAAGTAACAAACTGGTTGATCGCTG  >  W3110S.gb/3439798‑3439937

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