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
A6 F3 I0 R2	88	130.8	6963722	93.6%	6518043	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,065,007	T→G	5.7%	V416V (GTT→GTG)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,065,007	0	T	G	5.7%	448.2 / 15.1	155	V416V (GTT→GTG)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand): ref base T (79/67); new base G (4/5); total (83/72)
Fisher's exact test for biased strand distribution p-value = 7.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 178 total aligned reads displayed.

AATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCA  >  minE/2064937‑2065077

aaTACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        <  1:5053871/71‑1 (MQ=255)

 aTACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:1079908/1‑70 (MQ=255)

 aTACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:6876392/1‑70 (MQ=255)

 aTACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:3788427/1‑70 (MQ=255)

 aTACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:4820853/1‑70 (MQ=255)

   acacCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGa                                                                      >  1:5673221/1‑70 (MQ=255)

    cacCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:1236955/71‑1 (MQ=255)

     acCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaa                                                                   <  1:1101925/71‑1 (MQ=255)

      ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAATGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:1029277/69‑1 (MQ=255)

      ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                  <  1:1062831/71‑1 (MQ=255)

      ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:2005012/69‑1 (MQ=255)

          ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                              <  1:1357052/71‑1 (MQ=255)

          ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                              <  1:627763/71‑1 (MQ=255)

             tGGCTTGGAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:365657/62‑1 (MQ=255)

             tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:6052850/62‑1 (MQ=255)

             tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:3884138/62‑1 (MQ=255)

             tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:650810/62‑1 (MQ=255)

               gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                          <  1:4265932/70‑1 (MQ=255)

               gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                          <  1:5697636/70‑1 (MQ=255)

               gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                          <  1:928443/70‑1 (MQ=255)

               gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                          <  1:3531724/70‑1 (MQ=255)

                   gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgcc                                                     >  1:1719058/1‑71 (MQ=255)

                   gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgcc                                                     >  1:486590/1‑71 (MQ=255)

                   gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgc                                                      >  1:3328902/1‑70 (MQ=255)

                    caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                    >  1:181924/4‑71 (MQ=16)

                    caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                    >  1:593885/4‑71 (MQ=16)

                    cAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgccg                                                    <  1:1642067/71‑1 (MQ=255)

                     aGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                    <  1:5513543/54‑1 (MQ=255)

                       ttCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTgg                                                 >  1:2477734/1‑71 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAGCATCGGTCTGATGAAAGCGGTTg                                                                       >  1:5899465/1‑47 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTg                                                                       >  1:2745915/1‑47 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTg                                                                       >  1:4595386/1‑47 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTg                                                                       >  1:4948457/1‑47 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                  >  1:5387391/1‑52 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                  >  1:353584/1‑52 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                  >  1:1324349/1‑52 (MQ=255)

                         ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                                >  1:2903113/1‑70 (MQ=255)

                          cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGaa                                                            <  1:5050473/57‑1 (MQ=255)

                          cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGtt                                               <  1:3299949/70‑1 (MQ=255)

                           ttGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTa                                              >  1:5458637/1‑70 (MQ=255)

                            tGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTAc                                             >  1:2791913/1‑70 (MQ=255)

                             gACCTGATTCAGGATGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                     >  1:6434216/1‑45 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGa                                                                      >  1:691130/1‑44 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                     >  1:5023907/1‑45 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                     >  1:476270/1‑45 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                     >  1:3934440/1‑45 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                     >  1:3189736/1‑45 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                     >  1:6305556/1‑45 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTgg                                                 >  1:4675642/1‑65 (MQ=255)

                             gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTg                                                  >  1:849608/1‑64 (MQ=255)

                                cTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGt                                         <  1:3069935/70‑1 (MQ=255)

                                cTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                         <  1:6131862/70‑3 (MQ=12)

                                  gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtct                                      >  1:4451688/1‑71 (MQ=255)

                                  gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtc                                       >  1:5464138/1‑70 (MQ=255)

                                  gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAACGCCGTGGTTACAAGTtct                                      >  1:3737742/1‑71 (MQ=255)

                                   aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:2594903/1‑36 (MQ=255)

                                   aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:2879053/1‑36 (MQ=255)

                                   aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:2981297/1‑36 (MQ=255)

                                   aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt                                                                        >  1:5646510/1‑36 (MQ=255)

                                   aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtc                                       <  1:1970486/69‑1 (MQ=255)

                                   aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGCTGATAAATTCg                                                              <  1:4995951/46‑1 (MQ=255)

                                     ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcg                                    >  1:2251713/2‑69 (MQ=255)

                                       aGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCAc                                  <  1:5898393/70‑1 (MQ=255)

                                        ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                <  1:6186843/71‑1 (MQ=255)

                                        ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                <  1:1301026/71‑1 (MQ=255)

                                        ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                <  1:5725593/71‑1 (MQ=255)

                                        ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                <  1:4786549/71‑1 (MQ=255)

                                        ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                <  1:4123415/71‑1 (MQ=255)

                                          aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTAc                              <  1:6587845/71‑1 (MQ=255)

                                            ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                              <  1:2959563/37‑1 (MQ=255)

                                            ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                              <  1:555968/37‑1 (MQ=255)

                                            ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                              <  1:470093/37‑1 (MQ=255)

                                            ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                              <  1:799211/37‑1 (MQ=255)

                                             gCAACATCGTTCTGATGATAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCa                           <  1:377667/71‑1 (MQ=255)

                                             gCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCa                           <  1:5347566/71‑1 (MQ=255)

                                                aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                    <  1:1507474/59‑1 (MQ=255)

                                                aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                        <  1:1828410/71‑1 (MQ=255)

                                                  aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtg                      >  1:1432374/1‑71 (MQ=255)

                                                     ggTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCaa                          >  1:2589102/1‑64 (MQ=255)

                                                     ggTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                   >  1:2659628/1‑71 (MQ=255)

                                                     ggTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                   >  1:6804802/1‑71 (MQ=255)

                                                       tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtct                                      >  1:416159/1‑50 (MQ=255)

                                                       tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                   >  1:3948830/1‑69 (MQ=255)

                                                       tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                   >  1:663752/1‑69 (MQ=255)

                                                       tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                   >  1:4958472/1‑69 (MQ=255)

                                                        cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtgg                     >  1:15568/1‑66 (MQ=255)

                                                          gatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                <  1:4035737/53‑1 (MQ=255)

                                                           atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaac                                          >  1:5141410/1‑41 (MQ=255)

                                                           atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                     >  1:6143990/1‑47 (MQ=255)

                                                           atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCa                                   >  1:6260242/1‑49 (MQ=255)

                                                           atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                       <  1:6137594/61‑1 (MQ=255)

                                                           atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                       <  1:2327259/61‑1 (MQ=255)

                                                            tgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                            >  1:4294136/1‑55 (MQ=255)

                                                             gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt            >  1:3396338/1‑70 (MQ=255)

                                                               aaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAg         >  1:4452565/1‑71 (MQ=255)

                                                                    gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                       <  1:2329383/52‑1 (MQ=255)

                                                                    gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGa     >  1:3019055/1‑70 (MQ=255)

                                                                    gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGAt    >  1:6370581/1‑71 (MQ=255)

                                                                     ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc   <  1:5651283/71‑1 (MQ=255)

                                                                      tGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCa  >  1:6151798/1‑71 (MQ=255)

AATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCA  >  minE/2064937‑2065077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A