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 F28 I1 R2	328	63.0	4687567	98.0%	4593815	65.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,714,423	C→T	H61Y (CAC→TAC)	atpI →	ATP synthase, membrane‑bound accesory subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,714,423	0	C	T	100.0%	185.4 / NA	61	H61Y (CAC→TAC)	atpI	ATP synthase, membrane‑bound accesory subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (34/27); total (34/27)

TCTCTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGT  >  W3110S.gb/3714355‑3714490

tctcTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   <  1:1940117/71‑1 (MQ=255)

  tctGCACTAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:592975/1‑69 (MQ=255)

  tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:1148355/1‑69 (MQ=255)

  tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:3591400/1‑69 (MQ=255)

  tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:3766316/1‑69 (MQ=255)

  tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:3199404/1‑69 (MQ=255)

  tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:3813512/1‑69 (MQ=255)

  tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:476574/1‑69 (MQ=255)

      cAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg                                                             <  1:1366979/71‑1 (MQ=255)

        aTAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa                                                           <  1:147284/71‑1 (MQ=255)

         tAAGCGGGGGCCTGGGAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa                                                           <  1:3021274/70‑1 (MQ=255)

         tAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa                                                           <  1:2479751/70‑1 (MQ=255)

            gCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATaca                                                       <  1:232304/71‑1 (MQ=255)

                       gCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAgg                                            >  1:4338156/1‑71 (MQ=255)

                        cAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGc                                           <  1:3224967/71‑1 (MQ=255)

                          gTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa                                                           <  1:4672320/53‑1 (MQ=255)

                           tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTTGCGTTAc                                                                   <  1:1277608/44‑1 (MQ=38)

                           tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   <  1:3127039/44‑1 (MQ=255)

                            cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa                                                           >  1:3361849/1‑51 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:2428871/1‑71 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:3563028/1‑71 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:3535542/1‑71 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:1426789/1‑71 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:2228510/1‑71 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:4257381/1‑71 (MQ=255)

                             tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt                                      >  1:4293617/1‑71 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:3845048/1‑40 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc                                                                   >  1:3094101/1‑40 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATa                                                         >  1:4219769/1‑50 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTgg                                    >  1:1837594/1‑71 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTgg                                    >  1:1804915/1‑71 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTgg                                    >  1:1781775/1‑71 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTgg                                    >  1:4588593/1‑71 (MQ=255)

                               tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTg                                     <  1:4086787/70‑1 (MQ=255)

                                   ccTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGc                                   <  1:1186937/68‑1 (MQ=255)

                                       aagTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGa                              <  1:4549468/67‑1 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAg                                                                >  1:783631/1‑35 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAg                                                                >  1:162194/1‑35 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAg                                                                >  1:1837276/1‑35 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGa                              <  1:1339035/69‑1 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGa                              <  1:4407065/69‑1 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACa                            >  1:884585/1‑71 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACa                            <  1:620075/71‑1 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACa                            >  1:4020885/1‑71 (MQ=255)

                                       aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCACATACACCAGCGAAAGGCCGGGTGGCCTGGa                              <  1:3753276/69‑1 (MQ=255)

                                         gTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACAtt                          <  1:2921824/71‑1 (MQ=255)

                                            ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCg                        <  1:3847166/70‑1 (MQ=255)

                                            ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCg                        >  1:214660/1‑70 (MQ=255)

                                              gTTTATGATATTTGCCTGGCGTTACCAGGCCCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCa                      <  1:4608166/70‑1 (MQ=255)

                                                      tatTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCa                      <  1:1670958/62‑1 (MQ=255)

                                                        tttGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTg                                >  1:1385362/1‑50 (MQ=255)

                                                        tttGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCAtt                    >  1:3685869/1‑62 (MQ=255)

                                                          tGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt         >  1:4200201/1‑71 (MQ=255)

                                                          tGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt         >  1:1224252/1‑71 (MQ=255)

                                                          tGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCtt         >  1:3526649/1‑71 (MQ=255)

                                                             cTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCa      <  1:363317/71‑1 (MQ=255)

                                                             cTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCa      <  1:4633398/71‑1 (MQ=255)

                                                             cTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCa      <  1:2236426/71‑1 (MQ=255)

                                                                gCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCaa     <  1:577449/69‑1 (MQ=255)

                                                                 cGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGt  <  1:1853118/71‑1 (MQ=255)

                                                                 cGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGt  <  1:2783948/71‑1 (MQ=255)

TCTCTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGT  >  W3110S.gb/3714355‑3714490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A