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 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,816,309	T→C	22.0%	intergenic (‑52/‑34)	soxS ← / → soxR	DNA‑binding transcriptional dual regulator/DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,816,309	0	T	C	22.0%	111.4 / 28.2	59	intergenic (‑52/‑34)	soxS/soxR	DNA‑binding transcriptional dual regulator/DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing
Reads supporting (aligned to +/- strand): ref base T (18/28); new base C (5/8); total (23/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCT  >  minE/2816239‑2816377

taatTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGtat                                                                      <  1:1886029/71‑1 (MQ=255)

  atTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATaa                                                                    <  1:1394554/71‑1 (MQ=255)

   ttttCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAAt                                                                   <  1:1026491/71‑1 (MQ=255)

   ttttCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAAt                                                                   <  1:1203113/71‑1 (MQ=255)

     ttCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAAtt                                                                  <  1:2153303/70‑1 (MQ=255)

       cTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTTCAATTCCt                                                               >  1:44646/1‑71 (MQ=255)

          aTGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTc                                                              >  1:2792066/1‑69 (MQ=255)

           tGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAg                                                           >  1:3388412/1‑71 (MQ=255)

              gACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGtt                                                         >  1:3841374/1‑70 (MQ=255)

               aCATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCaa                                                            <  1:1228145/66‑1 (MQ=255)

               aCATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTa                                                        <  1:1388367/70‑1 (MQ=255)

                cATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAAc                                                      >  1:3515915/1‑71 (MQ=255)

                 aTAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAAt                                                                   <  1:924978/57‑1 (MQ=255)

                 aTAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACt                                                     <  1:1824001/71‑1 (MQ=255)

                  tAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGtat                                                                      <  1:2019392/53‑1 (MQ=255)

                  tAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATaa                                                                    <  1:2035157/55‑1 (MQ=255)

                  tAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACtt                                                    <  1:1822051/71‑1 (MQ=255)

                  tAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTc                                                              >  1:3037445/1‑61 (MQ=255)

                   aaaTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACtt                                                    >  1:549428/1‑70 (MQ=255)

                    aaTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACtt                                                    >  1:3599146/1‑69 (MQ=255)

                    aaTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTg                                                   <  1:2235975/70‑1 (MQ=255)

                    aaTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTg                                                   <  1:295977/70‑1 (MQ=255)

                    aaTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTg                                                   <  1:3862834/70‑1 (MQ=255)

                    aaTCTGCCTCTTTTCAGTGTTCAGTTAGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACtt                                                    >  1:1010609/1‑69 (MQ=255)

                          ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTaa                                             <  1:395971/70‑1 (MQ=255)

                          ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTaaa                                            <  1:174973/71‑1 (MQ=255)

                             ctTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTcc                                                                >  1:697292/1‑48 (MQ=255)

                             ctTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTcc                                                                >  1:268550/1‑48 (MQ=255)

                             ctTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTaaa                                            >  1:3718592/1‑68 (MQ=255)

                              ttttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGc                                          <  1:3561743/69‑1 (MQ=255)

                                  cAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTg                                                   >  1:1566746/1‑56 (MQ=255)

                                  cAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGAttt                                     <  1:2073810/70‑1 (MQ=255)

                                  cAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGCGAttt                                     <  1:3434847/70‑1 (MQ=255)

                                   aGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTa                                    <  1:1174460/70‑1 (MQ=255)

                                   aGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTa                                    <  1:1362476/70‑1 (MQ=255)

                                       ttCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTaa                                             >  1:2531342/1‑57 (MQ=255)

                                        tCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAg                                                           <  1:3558980/42‑1 (MQ=255)

                                          aGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGaa                               >  1:1780097/1‑68 (MQ=255)

                                          aGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGaa                               >  1:1050262/1‑68 (MQ=255)

                                          aGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAg                            <  1:3210703/71‑1 (MQ=255)

                                           gTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCa                                                             <  1:1557473/37‑1 (MQ=255)

                                             tCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAg                                                           >  1:2855784/1‑37 (MQ=255)

                                               gTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGaa                          <  1:2688668/68‑1 (MQ=255)

                                               gTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAAt                        <  1:81444/70‑1 (MQ=255)

                                               gTTAATTCATCTGTTGGGGAGTACAATTCCTCAGGTTAACTTGAGGTaa                                             <  1:2518323/49‑1 (MQ=39)

                                                 tAATTCATCTGTTGGGTAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGAttt                                     <  1:616110/55‑1 (MQ=255)

                                                 tAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGAttt                                     <  1:2523463/55‑1 (MQ=255)

                                                   aTTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTAccc                   >  1:3119963/1‑71 (MQ=255)

                                                        tCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGa                                                  <  1:358753/35‑1 (MQ=255)

                                                        tCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTa                                              >  1:3187609/1‑39 (MQ=255)

                                                         cTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCAt              >  1:2402764/1‑70 (MQ=255)

                                                         cTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCAt              >  1:3900526/1‑70 (MQ=255)

                                                          tGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCAtt             >  1:2307010/1‑70 (MQ=255)

                                                            ttGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTa            <  1:2427011/69‑1 (MQ=255)

                                                            ttGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTa            <  1:3641322/69‑1 (MQ=255)

                                                            ttGGGGAGTACAATTCCTCAAGTTAACTTGAGGTa                                              <  1:3364909/35‑1 (MQ=255)

                                                            ttGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCAtt             <  1:3400342/68‑1 (MQ=255)

                                                              ggggAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAg         <  1:3251350/70‑1 (MQ=255)

                                                               gggAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGaa                          <  1:3640831/52‑1 (MQ=255)

                                                                  aGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGaa                          <  1:2938647/49‑1 (MQ=255)

                                                                   gTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCgctgc   >  1:2934453/1‑71 (MQ=255)

                                                                    tataATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGa                           <  1:458327/46‑1 (MQ=255)

                                                                     ataATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCgctgct  <  1:2567131/70‑1 (MQ=255)

TAATTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCT  >  minE/2816239‑2816377

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A