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	3,204,990	T→C	28.1%	intergenic (‑78/‑129)	ygiP ← / → ttdA	predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,204,990	0	T	C	28.1%	145.7 / 74.2	96	intergenic (‑78/‑129)	ygiP/ttdA	predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand): ref base T (23/46); new base C (13/14); total (36/60)
Fisher's exact test for biased strand distribution p-value = 2.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

Only 100 of 107 total aligned reads displayed.

ATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACAT  >  W3110S.gb/3204921‑3205059

aTCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATattcatt                                                                      >  1:3315003/1‑71 (MQ=255)

      aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAtt                                                                <  1:1070100/71‑1 (MQ=255)

          gtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGGTCTGGCGCAATATTCATTCTTATTTTc                                                             >  1:1068606/1‑70 (MQ=255)

          gtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTcg                                                            >  1:2762092/1‑71 (MQ=255)

           tgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAt                                                                 <  1:4105959/65‑1 (MQ=255)

             aTAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTcgcg                                                          <  1:2564894/70‑1 (MQ=255)

             aTAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGt                                                         <  1:2555/71‑1 (MQ=255)

              tAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGtt                                                        <  1:3910863/71‑1 (MQ=255)

                aGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTg                                                       <  1:2862226/70‑1 (MQ=255)

                       tgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAt                                                                 <  1:3826727/53‑1 (MQ=255)

                         tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAtt                                                                <  1:3984246/52‑1 (MQ=255)

                         tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAtt                                                                <  1:4184410/52‑1 (MQ=255)

                         tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAtt                                                                <  1:158345/52‑1 (MQ=255)

                         tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAAc                                             >  1:419175/1‑71 (MQ=255)

                         tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTAtttt                                                              <  1:250676/54‑1 (MQ=255)

                         tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGa                                                      >  1:3895861/1‑62 (MQ=255)

                          aTTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa                                                                  <  1:3391822/49‑1 (MQ=255)

                          aTTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTa                                                                  <  1:3735780/49‑1 (MQ=255)

                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCtt                                                                   <  1:77249/47‑1 (MQ=255)

                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCtt                                                                   <  1:2243074/47‑1 (MQ=255)

                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGa                                               <  1:3844138/67‑1 (MQ=255)

                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTg                                           >  1:437458/1‑71 (MQ=255)

                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGt                                          <  1:1856793/70‑1 (MQ=255)

                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGt                                          >  1:3865045/1‑70 (MQ=255)

                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAAATGt                                          >  1:4290499/1‑70 (MQ=255)

                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTAtt                                                                >  1:424171/1‑48 (MQ=255)

                              cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGtt                                         <  1:2575902/70‑1 (MQ=255)

                              cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGtt                                         <  1:3606802/70‑1 (MQ=255)

                              cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGtt                                         <  1:671826/70‑1 (MQ=255)

                               gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTa                                        <  1:1266773/70‑1 (MQ=255)

                               gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTa                                        <  1:3538963/70‑1 (MQ=255)

                               gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTa                                        <  1:3533754/70‑1 (MQ=255)

                                cAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGAtt                                                    <  1:832055/57‑1 (MQ=255)

                                 aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTa                                                                  <  1:605852/42‑1 (MQ=255)

                                 aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTa                                                                  <  1:3387070/42‑1 (MQ=255)

                                 aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                       >  1:626083/1‑69 (MQ=255)

                                  aaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                       >  1:2553532/1‑68 (MQ=255)

                                  aaaCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCa                                                  >  1:859696/1‑57 (MQ=255)

                                  aaaCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAAtt                                     >  1:2499018/1‑70 (MQ=255)

                                   aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCtt                                                                   <  1:2109398/39‑1 (MQ=255)

                                   aaCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTa                                    >  1:4527543/1‑70 (MQ=255)

                                    aCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCAc                                                 >  1:3588475/1‑56 (MQ=255)

                                    aCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACa                                  <  1:4086989/71‑1 (MQ=255)

                                     cATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGtt                                                        <  1:2540618/48‑1 (MQ=255)

                                     cATTGCCATTCCCTG‑‑CTGGCGCAATATTCATTCTTATTTTc                                                             >  1:1997603/1‑41 (MQ=37)

                                       ttGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGtt                                                        <  1:1056168/46‑1 (MQ=255)

                                       ttGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACatat                               <  1:1720521/71‑1 (MQ=255)

                                         gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATAtt                              <  1:265862/70‑1 (MQ=255)

                                         gCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATAtt                              <  1:2683793/70‑1 (MQ=255)

                                         gCCATTCACTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                       >  1:292364/1‑61 (MQ=255)

                                          ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACata                                <  1:27783/67‑1 (MQ=255)

                                            aTTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGaa                                              >  1:4036025/1‑51 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGtt                                                        <  1:2986257/40‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa                                                      <  1:4565132/42‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGAtt                                                    <  1:1580816/44‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCa                                                  <  1:4319254/46‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCAc                                                 <  1:249551/47‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGa                                               <  1:4336186/49‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGtt                                         <  1:47405/55‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCACTCTTATTTTcg                                                            <  1:4367566/36‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGa                                                      <  1:611384/42‑1 (MQ=255)

                                             ttCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCCTTGa                                                      <  1:2319123/42‑1 (MQ=38)

                                              tCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa                                                      >  1:3624110/1‑41 (MQ=255)

                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa                                                      >  1:3290725/1‑40 (MQ=255)

                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCa                                                  >  1:1166128/1‑44 (MQ=255)

                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGt                        >  1:2112168/1‑70 (MQ=255)

                                               cccTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGa                                                      >  1:1328321/1‑40 (MQ=255)

                                               cccTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTa                                    <  1:3477407/58‑1 (MQ=255)

                                               cccTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACg                          >  1:1902536/1‑68 (MQ=255)

                                               cacTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACgg                         >  1:1683480/3‑69 (MQ=255)

                                                ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGtt                                                        <  1:2403342/37‑1 (MQ=255)

                                                  tGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                       >  1:3009178/1‑52 (MQ=255)

                                                    ctctGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTg                                           >  1:432383/1‑46 (MQ=255)

                                                     tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaaa                  >  1:3769796/1‑70 (MQ=255)

                                                     tatGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaaa                  >  1:333563/3‑70 (MQ=255)

                                                      ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCa                                                  >  1:1101500/1‑37 (MQ=255)

                                                      ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTAc                                   <  1:63636/52‑1 (MQ=255)

                                                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGaa                                              >  1:3208475/1‑37 (MQ=255)

                                                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGaa                                              >  1:1020277/1‑37 (MQ=255)

                                                            cAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa          <  1:2082253/71‑1 (MQ=255)

                                                              atatTCATTCTTATTTTCGCGTTGATTCCCGAACTGtt                                         <  1:2457692/38‑1 (MQ=255)

                                                              atatTCATTCTTATTTTCGCGTTGATTCACGAACTg                                           <  1:1395452/36‑1 (MQ=255)

                                                              atatTCATTCTTATTTTCGCGTTGATTCACGAACTGtt                                         <  1:2642234/38‑1 (MQ=255)

                                                              atatTCATTCTTATTTTCGCGTTGATTCACGAACTGt                                          <  1:2467342/37‑1 (MQ=255)

                                                              atatTCACTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                       >  1:1908221/1‑40 (MQ=255)

                                                               tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAAt                                      <  1:195633/40‑1 (MQ=255)

                                                               tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACa                                  <  1:1634313/44‑1 (MQ=255)

                                                               tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACg                          <  1:1294662/52‑1 (MQ=255)

                                                               tatTCATTCTTATTTTCGAGTTGATTCACGAACTGTTAATTACATAtt                              <  1:1488928/48‑1 (MQ=255)

                                                               tatTCATTCTTATTATCGCGTTGATTCACGAAATGTTAATTa                                    <  1:4102041/42‑1 (MQ=38)

                                                                attcattcTTATTTTCGCGTTGATTCACGAACTGTTaa                                       >  1:2589631/1‑38 (MQ=255)

                                                                attcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa          <  1:3682147/67‑1 (MQ=255)

                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAATCca     <  1:386206/71‑1 (MQ=255)

                                                                 ttcactcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACca     >  1:808243/1‑71 (MQ=255)

                                                                  tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaaaaaa               >  1:1435265/1‑60 (MQ=255)

                                                                   cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACcaca   >  1:1081827/1‑71 (MQ=255)

                                                                   cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACcac    <  1:1307258/70‑1 (MQ=255)

                                                                    attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACcac    <  1:208867/69‑1 (MQ=255)

                                                                    attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACAt  <  1:4269479/71‑1 (MQ=255)

                                                                    attcTTATTTTAGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACAt  <  1:1038915/71‑1 (MQ=255)

ATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACAT  >  W3110S.gb/3204921‑3205059

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