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
A3 F2 I1 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	Exported	217,996	A→T	79.8%	intergenic (‑88/‑18)	yafU ← / → yafF	predicted inner membrane protein/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	217,996	0	A	T	79.8%	460.4 / 105.1	207	intergenic (‑88/‑18)	yafU/yafF	predicted inner membrane protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (18/24); new base T (89/76); total (107/100)
Fisher's exact test for biased strand distribution p-value = 2.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 211 total aligned reads displayed.

CTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTT  >  Exported/217928‑218065

  gATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCg                                                                   >  1:134022/1‑71 (MQ=255)

   aTTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                                                  >  1:4721210/1‑71 (MQ=255)

   aTTTAACCGCAGAAAAGTTCGCCACAGGAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGc                                                                    <  1:2536454/69‑1 (MQ=255)

   aTTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGc                                                                    <  1:4158700/69‑1 (MQ=255)

      tAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCt                                                                <  1:1294206/70‑1 (MQ=255)

       aaCCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                                                               <  1:2028959/70‑1 (MQ=255)

          cGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACg                                                           <  1:4357549/71‑1 (MQ=255)

           gCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGt                                                          <  1:1187589/71‑1 (MQ=255)

            ctgagaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTg                                                         >  1:1464334/3‑71 (MQ=255)

              gaaaaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                                                       <  1:1425037/68‑1 (MQ=255)

               agaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                                                       <  1:4600385/70‑1 (MQ=255)

                 aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACg                                                           <  1:2818678/64‑1 (MQ=255)

                 aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                                                    <  1:4857679/71‑1 (MQ=255)

                 aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                                                    >  1:3358243/1‑71 (MQ=255)

                 aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                                                    >  1:2452531/1‑71 (MQ=255)

                 aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaa                                                     >  1:296888/1‑70 (MQ=255)

                 aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaa                                                     >  1:4839950/1‑70 (MQ=255)

                    ttCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCTCAGGCGTCTGGACGTGGTaatg                                                   <  1:2313760/69‑1 (MQ=255)

                      cGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaat                                                >  1:3005613/1‑70 (MQ=255)

                       gCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaatg                                               >  1:4191845/1‑70 (MQ=39)

                       gCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                                                   <  1:1666448/66‑1 (MQ=255)

                       gCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                                                   <  1:1526480/66‑1 (MQ=255)

                        ccACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:2614983/71‑1 (MQ=39)

                        ccACAGCAATCCGAAACCACTGGCACGTGGATAATAAGCTGCACAGGCGTCTGGACGt                                                          <  1:1691448/58‑1 (MQ=255)

                        ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:479102/71‑1 (MQ=255)

                         cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                                                 <  1:3630250/66‑1 (MQ=39)

                         cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                                                 <  1:2563555/66‑1 (MQ=39)

                         cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                                                 <  1:3734292/66‑1 (MQ=39)

                           caGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTgt                                                              <  1:2411341/51‑2 (MQ=255)

                           caGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac                                          >  1:2921521/1‑71 (MQ=255)

                           caGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac                                          <  1:1755055/71‑1 (MQ=255)

                            aGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTc                                                                 <  1:3297961/47‑1 (MQ=255)

                            aGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacg                                         <  1:2897789/71‑1 (MQ=255)

                            aGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAatgaatga                                              >  1:5182723/1‑66 (MQ=39)

                             gCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:5384363/1‑71 (MQ=255)

                              cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:153989/65‑1 (MQ=39)

                              cAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        <  1:4896869/70‑1 (MQ=255)

                                aTCCGAAATCTCTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGa                                                             <  1:2041284/47‑1 (MQ=255)

                                aTCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACtg                                     >  1:3663167/1‑70 (MQ=255)

                                aTCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgac                                          <  1:5408078/66‑1 (MQ=255)

                                 tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                                                  <  1:5121478/41‑1 (MQ=25)

                                 tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACtg                                     >  1:3170285/1‑69 (MQ=39)

                                 tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac                                          <  1:3384762/65‑1 (MQ=255)

                                  ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg                                                   <  1:4846693/55‑1 (MQ=255)

                                  ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:4957015/61‑1 (MQ=255)

                                  ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:5526294/61‑1 (MQ=255)

                                   cGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:2216808/60‑1 (MQ=255)

                                   cGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:349716/60‑1 (MQ=255)

                                   cGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCa                                   >  1:3812282/1‑70 (MQ=38)

                                   cGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCa                                   >  1:916147/1‑70 (MQ=38)

                                   cGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCa                                   >  1:3648158/1‑70 (MQ=255)

                                   cGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCt                                                                >  1:1119557/1‑41 (MQ=255)

                                    gAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:85915/1‑64 (MQ=255)

                                    gAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:5029932/1‑64 (MQ=255)

                                     aaaCCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACaaaa                                >  1:1000416/1‑71 (MQ=255)

                                       atcACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAAt                               >  1:4553976/3‑70 (MQ=255)

                                       aCCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCaaaa                                >  1:716916/1‑69 (MQ=39)

                                       aCCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAAt                               >  1:4678397/1‑70 (MQ=255)

                                       aCCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATa                              <  1:1218100/71‑1 (MQ=255)

                                         cACTGCCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTgtt                                                       <  1:3148034/44‑3 (MQ=37)

                                          aCTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaag                            >  1:1612584/1‑70 (MQ=255)

                                          aCTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaag                            >  1:1143779/1‑70 (MQ=255)

                                           cTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatga                                                  >  1:3975418/1‑47 (MQ=255)

                                            tGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgac                                          <  1:68454/54‑1 (MQ=255)

                                                 cGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATa                              <  1:3341300/61‑1 (MQ=255)

                                                  gTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGaaa                   >  1:5445949/1‑71 (MQ=255)

                                                   tGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                                                   <  1:2480457/38‑1 (MQ=255)

                                                   tGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                                                   <  1:1860410/38‑1 (MQ=255)

                                                   tGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                                                    <  1:394128/37‑1 (MQ=255)

                                                   tGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGa                     <  1:4260102/68‑1 (MQ=255)

                                                    ggAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                                                    <  1:4313151/36‑1 (MQ=255)

                                                     gagaATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGaaatg                 >  1:2136022/1‑68 (MQ=255)

                                                     gagaATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGaaatg                 >  1:2787229/1‑68 (MQ=255)

                                                     gagaATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGaaatg                 >  1:2582552/1‑68 (MQ=255)

                                                     gagaATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGAAACg                 >  1:441543/1‑70 (MQ=255)

                                                     gagaATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACg                 <  1:890734/70‑1 (MQ=255)

                                                      agaATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:2707129/1‑46 (MQ=255)

                                                        aaTAAGCTGCACTGGCGTCTGGACGTGGTaatgaatg                                               <  1:2337351/37‑1 (MQ=255)

                                                        aaTAAGCTGCACTGGCGTCTGGACGTGGTaatgaatg                                               <  1:585044/37‑1 (MQ=255)

                                                        aaTAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             <  1:3238460/39‑1 (MQ=255)

                                                         aTAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:3883483/1‑43 (MQ=255)

                                                         aTAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:3821537/1‑43 (MQ=255)

                                                         aTAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAga                                           >  1:5509808/1‑40 (MQ=255)

                                                          tAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                                             >  1:832923/1‑37 (MQ=255)

                                                          tAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:1812377/1‑42 (MQ=255)

                                                          tAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAga                                           >  1:4487658/1‑39 (MQ=255)

                                                          tAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaa                             >  1:3849266/1‑53 (MQ=255)

                                                          tAAGCTGCACAGTCGTCTGGACGTGGTAATGAATGAAgac                                          <  1:942508/40‑1 (MQ=255)

                                                          tAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAga                                           >  1:2228353/1‑39 (MQ=255)

                                                          tAAGCAGCACTGGAGTCTGGACGTGGTAATGAATGAAga                                           >  1:4099393/1‑39 (MQ=37)

                                                            aGCTGCACTGGCGTCTGGGCGTGGTAATGAATGAAGACGACTGCAAAAt                               >  1:3687921/1‑49 (MQ=38)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                                        >  1:3080510/1‑40 (MQ=255)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaag                            >  1:5621552/1‑52 (MQ=255)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaag                            >  1:3116917/1‑52 (MQ=255)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaa                             >  1:2125525/1‑51 (MQ=255)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaa                             >  1:2092121/1‑51 (MQ=255)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGaaatg                 >  1:1722551/1‑61 (MQ=255)

                                                            aGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATAAGAAGAGGaaatg                 >  1:103484/1‑61 (MQ=255)

                                                            aGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGaaa                   >  1:2262793/1‑61 (MQ=255)

                                                                    aGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATa                              <  1:5343441/42‑1 (MQ=255)

CTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGAGGAAACGCAGCAGAATTATTTT  >  Exported/217928‑218065

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