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
A1 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	614,426	C→T	76.6%	L349L (CTC→CTT)	entF →	enterobactin synthase multienzyme complex component, ATP‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	614,426	0	C	T	76.6%	119.6 / 38.0	64	L349L (CTC→CTT)	entF	enterobactin synthase multienzyme complex component, ATP‑dependent
Reads supporting (aligned to +/- strand): ref base C (3/12); new base T (20/29); total (23/41)
Fisher's exact test for biased strand distribution p-value = 2.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

TGCCGAACAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATACCCTGGC  >  W3110S.gb/614360‑614491

tGCCGAACAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAata                                                               <  1:1069306/71‑1 (MQ=255)

tGCCGAACAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAata                                                               <  1:874106/71‑1 (MQ=255)

tGCCGAACAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAata                                                               <  1:1197553/71‑1 (MQ=255)

tGCCGAACAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAata                                                               <  1:341234/71‑1 (MQ=255)

      aCAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAgg                                                         <  1:2088930/71‑1 (MQ=255)

      aCAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAgg                                                         <  1:3555239/71‑1 (MQ=255)

           ttGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTAttt                                                    <  1:3429983/71‑1 (MQ=255)

             gTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTg                                                   <  1:2724528/70‑1 (MQ=255)

             gTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTg                                                   <  1:410437/70‑1 (MQ=255)

              tCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGAt                                                 <  1:2948656/71‑1 (MQ=255)

              tCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGAt                                                 <  1:338809/71‑1 (MQ=255)

              tCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGAt                                                 <  1:1105157/71‑1 (MQ=255)

                         gggCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGa                                      <  1:1286945/71‑1 (MQ=255)

                         gggCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGa                                      <  1:1685680/71‑1 (MQ=255)

                                cGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCt                               <  1:1973442/71‑1 (MQ=255)

                                cGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCt                               <  1:3085538/71‑1 (MQ=255)

                                    aGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATg                           <  1:2010121/71‑1 (MQ=255)

                                    aGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATg                           <  1:661844/71‑1 (MQ=255)

                                    aGGTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATg                           <  1:3376010/71‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTAttt                                                    <  1:1529587/45‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTAttt                                                    <  1:2954315/45‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTAttt                                                    <  1:1289540/45‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTAttt                                                    <  1:1266569/45‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTAttt                                                    <  1:666083/45‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATg                           <  1:2432107/70‑1 (MQ=255)

                                     ggTGATGAACCGCTGTTTGGTCAGGTACTTAATATCAAGGTAttt                                                    <  1:2373488/45‑1 (MQ=38)

                                       tgatgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTa                                               <  1:2387620/48‑1 (MQ=255)

                                       tgatgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTa                                               <  1:2484075/48‑1 (MQ=255)

                                       tgatgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTa                                               <  1:2379735/48‑1 (MQ=255)

                                       tgatgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTa                                               <  1:1872939/48‑1 (MQ=255)

                                       tgatgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTa                                               <  1:1873467/48‑1 (MQ=255)

                                        gatgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGtt                         >  1:1388089/1‑69 (MQ=255)

                                         atgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTgg                                       <  1:2906405/54‑1 (MQ=255)

                                         atgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTgg                                       <  1:1555167/54‑1 (MQ=255)

                                         atgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTgg                                       <  1:1848205/54‑1 (MQ=255)

                                         atgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATg                           <  1:1738694/66‑1 (MQ=255)

                                         atgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAg                      >  1:619191/1‑71 (MQ=255)

                                         atgaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAg                      >  1:879790/1‑71 (MQ=255)

                                         atgaACCGCTGATTGTTCCGGTACTTAATATCAAGGTAttt                                                    <  1:301558/41‑1 (MQ=37)

                                           gaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGa                                                  >  1:387416/1‑41 (MQ=255)

                                           gaACCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGa                                                  >  1:3539030/1‑41 (MQ=255)

                                           gaACCGATGTTTGGTCCGGTACTTAATATCAAGGTATTTGa                                                  >  1:2883/1‑41 (MQ=38)

                                            aaCCGCTGTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGgcg                   >  1:2196669/1‑71 (MQ=255)

                                                   gTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGa                                      >  1:1184894/1‑45 (MQ=255)

                                                   gTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGa                                      >  1:122583/1‑45 (MQ=255)

                                                   gTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGa                                      >  1:2990423/1‑45 (MQ=255)

                                                   gTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGa                                      >  1:3573294/1‑45 (MQ=255)

                                                   gTTTGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGa                                      >  1:1518411/1‑45 (MQ=255)

                                                    tttGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCaa                <  1:1562132/66‑1 (MQ=255)

                                                    tttGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCaa                <  1:848393/66‑1 (MQ=255)

                                                      tGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCAt          <  1:1788207/70‑1 (MQ=255)

                                                      tGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATa         >  1:1259655/1‑71 (MQ=255)

                                                      tGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATa         >  1:3161798/1‑71 (MQ=255)

                                                      tGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATa         >  1:388391/1‑71 (MQ=255)

                                                      tGGTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATa         >  1:917810/1‑71 (MQ=255)

                                                        gTCCGGTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATAcc       <  1:1122906/71‑1 (MQ=255)

                                                          ccGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATACCCt     >  1:2244524/1‑71 (MQ=255)

                                                          ccGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATACCCt     >  1:2894470/1‑71 (MQ=255)

                                                          ccGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATACCCt     >  1:2428568/1‑71 (MQ=255)

                                                             gTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATAcc       >  1:1850253/1‑66 (MQ=255)

                                                             gTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATAcc       >  1:1221006/1‑66 (MQ=255)

                                                             gTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATAcc       >  1:1020537/1‑66 (MQ=255)

                                                             gTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATAcc       >  1:2098635/1‑66 (MQ=255)

                                                             gTACTTAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATACCCTGGc  <  1:3502521/71‑1 (MQ=255)

TGCCGAACAAATTGTCCGTGACAGCGGGCGAGCGGCAGGTGATGAACCGCTGTTTGGTCCGGTACTCAATATCAAGGTATTTGATTACCAACTGGATATTCCTGATGTTCAGGCGCAAACCCATACCCTGGC  >  W3110S.gb/614360‑614491

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