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 F8 I0 R2	296	77.6	4260404	88.1%	3753415	61.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,283,783	G→T	41.5%	L39M (CTG→ATG)	oxyR ←	DNA‑binding transcriptional dual regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,283,783	0	G	T	41.5%	79.4 / 60.0	65	L39M (CTG→ATG)	oxyR	DNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand): ref base G (16/22); new base T (16/11); total (32/33)
Fisher's exact test for biased strand distribution p-value = 2.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.56e-01

ATTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGC  >  minE/2283713‑2283851

aTTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAg                                                                      >  1:41328/1‑71 (MQ=255)

 ttCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAg                                                                      >  1:219679/1‑70 (MQ=255)

 ttCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGc                                                                     >  1:2489353/1‑71 (MQ=255)

 ttCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGc                                                                     >  1:225218/1‑71 (MQ=255)

   cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCt                                                                    >  1:3571837/1‑70 (MQ=255)

   cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCt                                                                    <  1:245560/70‑1 (MQ=255)

   cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCt                                                                    <  1:1875117/70‑1 (MQ=255)

       ccTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGa                                                               <  1:1908779/71‑1 (MQ=255)

       ccTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGa                                                               <  1:2225863/71‑1 (MQ=255)

           ggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAtt                                                            <  1:3802265/70‑1 (MQ=255)

            gTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTg                                                          <  1:4216951/71‑1 (MQ=255)

            gTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTg                                                          <  1:3938871/71‑1 (MQ=255)

                 caacaCTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGc                                                     >  1:2051849/1‑71 (MQ=255)

                 caacaCTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTg                                                          <  1:504835/66‑1 (MQ=255)

                  aacaCTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCt                                                    <  1:3957424/71‑1 (MQ=255)

                   acacTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCt                                                    <  1:433997/70‑1 (MQ=255)

                    cacTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTaa                                                  <  1:79954/71‑1 (MQ=255)

                    cacTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTaa                                                  <  1:762580/71‑1 (MQ=255)

                    cacTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTaa                                                  <  1:6538/71‑1 (MQ=255)

                      cTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGc                                                >  1:3094224/1‑71 (MQ=255)

                      cTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGc                                                >  1:987935/1‑71 (MQ=255)

                      cTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGc                                                >  1:1737133/1‑71 (MQ=255)

                         tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTc                                             >  1:4241247/1‑71 (MQ=255)

                         tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTc                                             >  1:3703378/1‑71 (MQ=255)

                         tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTc                                             >  1:3819799/1‑71 (MQ=255)

                         tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTc                                             >  1:2055474/1‑71 (MQ=255)

                         tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTc                                             >  1:1749532/1‑71 (MQ=255)

                         tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTc                                             >  1:4118125/1‑71 (MQ=255)

                           cGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCgg                                           <  1:2677352/71‑1 (MQ=255)

                           cGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCgg                                           <  1:2898149/71‑1 (MQ=255)

                             gCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCggct                                         <  1:3889375/71‑1 (MQ=255)

                                 gTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCggctggct                                     <  1:3416762/71‑1 (MQ=255)

                                 gTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCggctggc                                      >  1:2637834/1‑70 (MQ=255)

                                 gTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCggctggct                                     <  1:3945337/71‑1 (MQ=255)

                                 gTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCggctggct                                     <  1:2446381/71‑1 (MQ=255)

                                    cGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGc                                                     >  1:3297645/1‑52 (MQ=255)

                                    cGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGc                                                     >  1:3821216/1‑52 (MQ=255)

                                    cGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAAc                                  >  1:361850/1‑71 (MQ=255)

                                     gCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACg                                 <  1:1529828/71‑1 (MQ=255)

                                      cTCCATCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:2540098/71‑1 (MQ=255)

                                      cTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTg                                                          <  1:1722005/45‑1 (MQ=255)

                                      cTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:3393218/71‑1 (MQ=255)

                                      cTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt                                <  1:2015334/71‑1 (MQ=255)

                                        ccAGCAACATCACGCCCAGCTCATCTTCCATCTTAc                                                                 >  1:2404437/1‑36 (MQ=255)

                                        ccAGCAACATCACGCCCAGCTCATCTTCCATCTTAc                                                                 >  1:2948156/1‑36 (MQ=255)

                                             aaCATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCggctggct                                     <  1:255335/59‑1 (MQ=255)

                                                aTCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATc                      <  1:591425/71‑1 (MQ=255)

                                                aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATc                      >  1:3533093/1‑71 (MQ=255)

                                                aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATc                      >  1:3370363/1‑71 (MQ=255)

                                                   aCGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTg                    >  1:4124436/1‑70 (MQ=255)

                                                   aCGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGc                   >  1:1550806/1‑71 (MQ=255)

                                                   aCGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGc                   >  1:2930986/1‑71 (MQ=255)

                                                     gCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTTGCTAACGTGGCAGGAATCTGCCg                 >  1:2497178/1‑71 (MQ=255)

                                                     gCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCg                 >  1:3693620/1‑71 (MQ=255)

                                                     gCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCg                 >  1:3009912/1‑71 (MQ=255)

                                                     gCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCg                 >  1:1924404/1‑71 (MQ=255)

                                                     gCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCg                 >  1:1919475/1‑71 (MQ=255)

                                                     gCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCg                 >  1:997889/1‑71 (MQ=255)

                                                       ccAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCTTCGGCTGGCTAACGTGGCAGGAATCTGCCGCa               <  1:2847224/71‑1 (MQ=255)

                                                          gCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGa                         <  1:3857927/58‑1 (MQ=255)

                                                          gCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTCGCAGGa                         <  1:9527/58‑1 (MQ=255)

                                                             cATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCg          >  1:428218/1‑70 (MQ=255)

                                                              aTCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGaa        <  1:277312/71‑1 (MQ=255)

                                                                  tCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAAc                                  <  1:229464/41‑1 (MQ=255)

                                                                   ccAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATgg   >  1:660684/1‑71 (MQ=255)

                                                                    cAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGc  <  1:3982552/71‑1 (MQ=255)

                                                                    cAGCTTACGAATTTGCCCGCTAAGCGGCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGc  <  1:2526050/71‑1 (MQ=255)

ATTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAATGGC  >  minE/2283713‑2283851

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