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 F3 I0 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	483,191	T→C	20.5%	D146G (GAT→GGT)	acrB ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	483,191	0	T	C	20.5%	152.3 / 36.2	73	D146G (GAT→GGT)	acrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base T (29/29); new base C (9/6); total (38/35)
Fisher's exact test for biased strand distribution p-value = 5.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCACCCCTTGCTGCTG  >  W3110S.gb/483121‑483261

cGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCAt                                                                        >  1:3465169/1‑71 (MQ=255)

    cGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGgt                                                                    <  1:4380538/71‑1 (MQ=255)

      gCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGgtg                                                                   <  1:4566118/70‑1 (MQ=255)

         gATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGa                                                               >  1:3186721/1‑71 (MQ=255)

           tGGCATCTTTCATATTCGCCTCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              <  1:543816/70‑1 (MQ=255)

           tGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              <  1:2948661/70‑1 (MQ=255)

           tGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              <  1:4082501/70‑1 (MQ=255)

           tGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              <  1:1343820/70‑1 (MQ=255)

           tGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              <  1:2073890/70‑1 (MQ=255)

             gCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAAc                                                           <  1:1475570/71‑1 (MQ=255)

               aTCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              <  1:3476664/66‑1 (MQ=255)

                tCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGcc                                                        >  1:156496/1‑71 (MQ=255)

                tCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGcc                                                        >  1:2595647/1‑71 (MQ=255)

                 cTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGcc                                                        >  1:500207/1‑70 (MQ=255)

                  tttCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:4326669/1‑65 (MQ=255)

                  tttCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:1368509/1‑65 (MQ=255)

                  tttCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGa                                                      >  1:911829/1‑71 (MQ=255)

                  tttCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGa                                                      >  1:9508/1‑71 (MQ=255)

                  tttCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGa                                                      >  1:3574360/1‑71 (MQ=255)

                  tttCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGa                                                      >  1:1434018/1‑71 (MQ=255)

                  tttCATATTCGCCGACACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGa                                                      >  1:459981/1‑71 (MQ=255)

                    tCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGAt                                                              >  1:4587544/1‑61 (MQ=255)

                    tCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:848031/1‑63 (MQ=255)

                    tCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACgacgac                                                     >  1:4420974/1‑70 (MQ=255)

                    tCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGcc                                                        <  1:3757923/67‑1 (MQ=255)

                    tCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGAc                                                     <  1:181134/70‑1 (MQ=255)

                    tCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGAc                                                     <  1:1294840/70‑1 (MQ=255)

                      atatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAAc                                                  <  1:4316753/71‑1 (MQ=255)

                       tatTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            <  1:2068116/60‑1 (MQ=255)

                         ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGtt                                                                 <  1:3034874/53‑1 (MQ=255)

                         ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCAt                                               >  1:775446/1‑71 (MQ=255)

                         ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCAt                                               <  1:1870787/71‑1 (MQ=255)

                         ttCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCAt                                               >  1:3691270/1‑71 (MQ=255)

                           cgccgcCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATc                                              <  1:4509156/70‑1 (MQ=255)

                            gccgccACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATCa                                             <  1:1932382/70‑1 (MQ=255)

                               gccACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGAc                                                     <  1:3505192/59‑1 (MQ=255)

                               gccACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATaa                                                            >  1:4290259/1‑52 (MQ=255)

                               gccACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATa                                                             >  1:3172766/1‑51 (MQ=255)

                                  aCGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATCAGGAAgct                                      >  1:518721/1‑71 (MQ=255)

                                     tAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:3543508/1‑46 (MQ=255)

                                     tAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:2761513/1‑46 (MQ=255)

                                      aGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:3950490/1‑45 (MQ=255)

                                       gTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGaa                                         <  1:1099702/63‑1 (MQ=255)

                                       gTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGctgctg                                  <  1:3544395/70‑1 (MQ=255)

                                       gTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTTCTgg                                 <  1:3044291/71‑1 (MQ=255)

                                          ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAgg                                           >  1:1112984/1‑58 (MQ=255)

                                          ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatg                              <  1:2203348/71‑1 (MQ=255)

                                          ggAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatg                              <  1:2626368/71‑1 (MQ=255)

                                           gagaTATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatga                             >  1:2364438/1‑71 (MQ=255)

                                             gaTATCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGAtt                           <  1:3308198/71‑1 (MQ=255)

                                              atatCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGAttt                          <  1:3142593/71‑1 (MQ=255)

                                              atatCCTCCTGCGTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatga                             <  1:2067067/68‑1 (MQ=255)

                                               tatCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGa                                          <  1:3563464/54‑1 (MQ=255)

                                                atCCTCCTGCGTCATGGTGCCATCGGTGTTGATaa                                                            >  1:1579678/1‑35 (MQ=255)

                                                 tcctccTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACa                                                    <  1:2479051/42‑1 (MQ=255)

                                                 tcctccTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACCACCATCAGGAAGCTGCTGGATGATTtct                        >  1:67187/1‑70 (MQ=255)

                                                 tcctccTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTtct                        >  1:1801334/1‑70 (MQ=255)

                                                 tcctccTGCGTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTtctc                       <  1:4023949/71‑1 (MQ=255)

                                                      ctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatga                             <  1:1232273/60‑1 (MQ=255)

                                                      ctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCaa                     >  1:804367/1‑68 (MQ=255)

                                                      ctGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAAc                    <  1:1215752/69‑1 (MQ=255)

                                                        gCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgat                               >  1:1326875/1‑56 (MQ=255)

                                                        gCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCt                 >  1:3189194/1‑70 (MQ=255)

                                                         cGTCATGGTGCCATCGGTGTTGATAACGCCGACAAc                                                  >  1:3597864/1‑36 (MQ=255)

                                                         cGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCa               >  1:340043/1‑71 (MQ=255)

                                                         cGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCa               >  1:3707970/1‑71 (MQ=255)

                                                          gTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTtctc                       <  1:2814423/62‑1 (MQ=255)

                                                          gTCATGGTGCCACCGGTGTTGATAACGCCGACAACCATc                                              >  1:4112028/1‑39 (MQ=255)

                                                           tCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCt                 <  1:2587053/67‑1 (MQ=255)

                                                             aTGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCAcccc           >  1:2797180/1‑71 (MQ=255)

                                                             aTGGTGCCACCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTc                >  1:3251406/1‑66 (MQ=255)

                                                             aTGGTGCCACCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCAccc            <  1:2674641/70‑1 (MQ=255)

                                                                 tGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCa               >  1:350964/1‑63 (MQ=255)

                                                                   ccACCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCACTCCTtgctg     >  1:4284048/1‑71 (MQ=255)

                                                                      tCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatgat                            <  1:82348/45‑1 (MQ=255)

                                                                      tCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGgatgat                            <  1:87744/45‑1 (MQ=255)

                                                                      tCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCACCCCTTgctgct   >  1:1083969/1‑70 (MQ=255)

                                                                      tCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCACCCCTTGctgctg  <  1:2508179/71‑1 (MQ=255)

CGTACGGCTGATGGCATCTTTCATATTCGCCGCCACGTAGTCGGAGATATCCTCCTGCGTCATGGTGCCATCGGTGTTGATAACGCCGACAACCATCAGGAAGCTGCTGGATGATTTCTCAACGCTCACCCCTTGCTGCTG  >  W3110S.gb/483121‑483261

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