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	3,488,502	C→T	23.6%	L47L (CTG→TTG)	yijO →	predicted DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,488,502	0	C	T	23.6%	147.8 / 43.8	77	L47L (CTG→TTG)	yijO	predicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (27/31); new base T (8/10); total (36/41)
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

AGCAGTAACGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGATGTGCTGTACG  >  W3110S.gb/3488439‑3488565

agcagTAACGGCCCCGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAgg                                                          <  1:4085427/71‑1 (MQ=255)

    gTAACGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAg                                                      <  1:1755372/71‑1 (MQ=255)

     tAACGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTgg                                                              <  1:3400544/62‑1 (MQ=255)

     tAACGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGa                                                             <  1:992353/63‑1 (MQ=255)

       aCGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGTTgg                                                              >  1:1876105/1‑60 (MQ=255)

       aCGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAGttt                                                   >  1:3291391/1‑71 (MQ=255)

        cGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttg                                                  >  1:842966/1‑71 (MQ=255)

          gCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttgtt                                                <  1:4579294/71‑1 (MQ=255)

              ggTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATa                                            >  1:176876/1‑71 (MQ=255)

               gTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAGTTTGTTGATAc                                           <  1:3993289/71‑1 (MQ=255)

                  cccGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttg                                                  <  1:3218716/61‑1 (MQ=255)

                  cccGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttg                                                  <  1:2087816/61‑1 (MQ=255)

                  cccGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttg                                                  <  1:3899245/61‑1 (MQ=255)

                    cGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGgcg                                      >  1:4487190/1‑71 (MQ=255)

                       tCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTg                                   >  1:765432/1‑71 (MQ=255)

                        cTTGGGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttg                                                  <  1:1220314/55‑1 (MQ=255)

                        cTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAGTTTGTTGa                                              >  1:1845469/1‑59 (MQ=255)

                          tGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGc                                                                 <  1:51496/38‑1 (MQ=255)

                           gCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAg                                                      <  1:1200825/48‑1 (MQ=255)

                           gCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAg                                                      <  1:3347681/48‑1 (MQ=255)

                           gCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAg                                >  1:374236/1‑70 (MQ=255)

                             gTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGtt                                                    >  1:928213/1‑48 (MQ=255)

                             gTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCaa                             >  1:1656087/1‑71 (MQ=255)

                             gTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCaa                             <  1:2579202/71‑1 (MQ=255)

                              tATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCaa                             <  1:3924748/70‑1 (MQ=255)

                               aTCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAGTTTGTTGa                                              >  1:4106877/1‑52 (MQ=255)

                               aTCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACg                           >  1:3925123/1‑71 (MQ=255)

                               aTCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACg                           >  1:3097174/1‑71 (MQ=255)

                               aTCAGGTCGATTTTCCACGGCTGGAAATTGTGATGGAAGGTGAGttt                                                   >  1:4398511/1‑47 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTgg                                  <  1:4520251/63‑1 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTCAGTTTGTTGAt                                             <  1:2975201/52‑1 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttgtt                                                <  1:4041060/49‑1 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGa                                              >  1:348082/1‑51 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGa                                              >  1:2806629/1‑51 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCa                              <  1:4399134/67‑1 (MQ=255)

                                tCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGt                          >  1:4053459/1‑71 (MQ=255)

                                  aGGTCGATTTTCCATGGCTGGAAATTGTGTTGGAAGGTGAGttt                                                   >  1:1550314/1‑44 (MQ=38)

                                  aGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGttt                                                   >  1:3273100/1‑44 (MQ=255)

                                  aGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:342289/70‑1 (MQ=255)

                                  aGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:4417951/70‑1 (MQ=255)

                                   ggTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAg                       <  1:2093745/71‑1 (MQ=255)

                                    gTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGa                                              <  1:1077988/47‑1 (MQ=255)

                                     tCGATTTTCCACGGCTGGAAATTGTGTTGGAAGGTTAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:2526624/67‑1 (MQ=255)

                                      cGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTc                    >  1:1358373/1‑71 (MQ=255)

                                      cGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTc                    >  1:3490306/1‑71 (MQ=255)

                                      cGATTTTACACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTc                    >  1:959200/1‑71 (MQ=255)

                                       gATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGtt                                                    <  1:2201089/38‑1 (MQ=255)

                                        aTTTTCCACGGCTGGAAATTGTGTTGGAAGGTGAGTttg                                                  <  1:1625331/39‑1 (MQ=255)

                                         ttttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttg                                                  <  1:1467182/38‑1 (MQ=255)

                                         ttttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGa                                              <  1:2586142/42‑1 (MQ=255)

                                          tttCCACGGCTGGAAATTGTGTTGGAAGGTGAGTttgtt                                                >  1:1260547/1‑39 (MQ=255)

                                          tttCCACGGCTGGAAATTGTGCTGGAAGGTGAGtt                                                    <  1:1873084/35‑1 (MQ=255)

                                          tttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGtt                     >  1:4616924/1‑66 (MQ=255)

                                          tttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGtt                     >  1:4611652/1‑66 (MQ=255)

                                          tttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGtt                     >  1:287365/1‑66 (MQ=255)

                                          tttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCgg                >  1:4515304/1‑71 (MQ=255)

                                           ttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttgtt                                                >  1:4421720/1‑38 (MQ=255)

                                           ttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGc               >  1:1310555/1‑71 (MQ=255)

                                           ttCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGc               >  1:3309978/1‑71 (MQ=255)

                                            tCCACGGCTGGAAATTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGc               <  1:2072000/70‑1 (MQ=255)

                                            tCCACGGCTGGAAATTGTGCTGGAAGGTGAGTttgtt                                                >  1:1640635/1‑37 (MQ=255)

                                                 ggCTGGAAATTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGAtgtg         >  1:2178958/1‑71 (MQ=255)

                                                 ggCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGAtgtg         <  1:1012866/71‑1 (MQ=255)

                                                  gCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGATGTGc        >  1:3808564/1‑71 (MQ=255)

                                                    tGGAAATTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTGGa                                 <  1:2635934/44‑1 (MQ=255)

                                                      gAAATTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGt                          <  1:3044969/49‑1 (MQ=255)

                                                      gAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCaa                             >  1:474098/1‑46 (MQ=255)

                                                      gAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:49215/50‑1 (MQ=255)

                                                      gAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGa             <  1:2771454/62‑1 (MQ=255)

                                                      gAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGATGTGCTg      <  1:4462366/69‑1 (MQ=255)

                                                       aaaTTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAAc                            <  1:2076061/46‑1 (MQ=255)

                                                       aaaTTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:2574192/49‑1 (MQ=255)

                                                        aaTTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTa                        >  1:4635338/1‑49 (MQ=255)

                                                        aaTTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:1337716/48‑1 (MQ=255)

                                                        aaTTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGATGTGCTGTACg  >  1:1162586/1‑71 (MQ=255)

                                                         aTTGTGTTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:2842063/47‑1 (MQ=255)

                                                         aTTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGtt                         <  1:2086435/47‑1 (MQ=255)

                                                          ttGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGt                          <  1:2307745/45‑1 (MQ=255)

                                                               cTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGAtgtg         <  1:1880247/57‑1 (MQ=255)

AGCAGTAACGGCCCGGTGCCCGATCTTGCGTATCAGGTCGATTTTCCACGGCTGGAAATTGTGCTGGAAGGTGAGTTTGTTGATACCGGCGCTGGAGCAACGTTAGTTCCCGGCGATGTGCTGTACG  >  W3110S.gb/3488439‑3488565

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