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
A5 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,400,279	C→T	27.0%	P96P (CCG→CCA)	nuoJ ←	NADH:ubiquinone oxidoreductase, membrane subunit J

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,400,279	0	C	T	27.0%	109.7 / 42.2	63	P96P (CCG→CCA)	nuoJ	NADH:ubiquinone oxidoreductase, membrane subunit J
Reads supporting (aligned to +/- strand): ref base C (23/23); new base T (11/6); total (34/29)
Fisher's exact test for biased strand distribution p-value = 3.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.05e-01

ACCCTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAACCGCCCAGGT  >  W3110S.gb/2400213‑2400343

aCCCTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGAc                                                              >  1:4826301/1‑71 (MQ=255)

  ccTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCa                                                            <  1:1152218/71‑1 (MQ=255)

  ccTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCa                                                            <  1:3636098/71‑1 (MQ=255)

  ccTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCa                                                            <  1:3997583/71‑1 (MQ=255)

   cTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCaa                                                           <  1:672839/71‑1 (MQ=255)

      aTCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATc                                                         >  1:3683209/1‑70 (MQ=255)

      aTCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAAt                                                          <  1:2781224/69‑1 (MQ=255)

      aTCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATc                                                         <  1:1039918/70‑1 (MQ=255)

      aTCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATc                                                         <  1:2343789/70‑1 (MQ=255)

      aTCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATc                                                         <  1:4162157/70‑1 (MQ=255)

       tCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATcc                                                        >  1:3534861/1‑70 (MQ=255)

       tCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCca                                                       >  1:3151441/1‑71 (MQ=255)

       tCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCca                                                       >  1:5110454/1‑71 (MQ=255)

       tCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGAc                                                              >  1:3200582/1‑64 (MQ=255)

       tCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGAc                                                              >  1:1512623/1‑64 (MQ=255)

       tCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCca                                                       >  1:3709167/1‑71 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCcac                                                      <  1:1902191/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCcac                                                      <  1:1929814/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCcac                                                      <  1:3948522/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCcac                                                      <  1:1678920/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCcac                                                      <  1:476226/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCcac                                                      <  1:769969/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCcac                                                      <  1:2692168/70‑1 (MQ=255)

         gTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCcac                                                      <  1:1983621/70‑1 (MQ=255)

                 cGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGt                                             >  1:950033/1‑71 (MQ=255)

                 cGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGt                                             >  1:2983915/1‑71 (MQ=255)

                 cGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGt                                             >  1:3022549/1‑71 (MQ=255)

                 cGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGt                                             >  1:207758/1‑71 (MQ=255)

                  gAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGtt                                            >  1:2720145/1‑71 (MQ=255)

                  gAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGtt                                            >  1:1025256/1‑71 (MQ=255)

                         gCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGcc                                      <  1:3545286/70‑1 (MQ=255)

                          cGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCCACACCTGCGGTTTCAGCCAc                                    >  1:4754455/1‑71 (MQ=255)

                          cGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCAc                                    >  1:4538728/1‑71 (MQ=255)

                               aCAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCg                               <  1:880693/71‑1 (MQ=255)

                                cAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCacac                                                    >  1:1177059/1‑49 (MQ=255)

                                cAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCacac                                                    >  1:1873244/1‑49 (MQ=255)

                                  aTCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCCacac                                                    >  1:4563786/1‑47 (MQ=255)

                                  aTCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTc                            >  1:1838231/1‑71 (MQ=255)

                                  aTCACCACCAGCATGATGGCCGACAAAATTGCTGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTc                            >  1:3854056/1‑71 (MQ=255)

                                   tCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCca                                                       >  1:4631233/1‑43 (MQ=255)

                                   tCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCca                                                       >  1:2224388/1‑43 (MQ=255)

                                   tCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCca                                                       >  1:4539215/1‑43 (MQ=255)

                                     accaccAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCt                          <  1:1690369/70‑1 (MQ=255)

                                     accaccAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTg                         >  1:973043/1‑71 (MQ=255)

                                         ccaGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTg                         >  1:4948741/1‑67 (MQ=255)

                                         ccaGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTc                      >  1:247453/1‑70 (MQ=255)

                                         ccaGCATGATGGCCGACAAAATTGACGGACCAATCAACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTc                      >  1:2343854/1‑70 (MQ=255)

                                           aGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGAt                   <  1:1350859/71‑1 (MQ=255)

                                            gCATGATGGCCGACAAAATTGCCGGACCAATCcac                                                      >  1:2334242/1‑35 (MQ=255)

                                              atgatgGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCa                                     <  1:1294121/50‑1 (MQ=255)

                                              atgatgGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCa                                     <  1:4294712/50‑1 (MQ=255)

                                              atgatgGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTc                >  1:4544034/1‑71 (MQ=255)

                                                 atgGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTg              >  1:315915/1‑70 (MQ=255)

                                                 atgGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTg              <  1:656739/70‑1 (MQ=255)

                                                    gCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAAcc          <  1:4620569/71‑1 (MQ=255)

                                                    gCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAAcc          <  1:4523211/71‑1 (MQ=255)

                                                       gACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTg                         <  1:2339302/53‑1 (MQ=255)

                                                       gACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAACCGcc       <  1:647116/71‑1 (MQ=255)

                                                         cAAAATTGCTGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAACCGcc       >  1:554708/1‑69 (MQ=255)

                                                            aaTTGCTGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAACCGCCCAGGt  >  1:1817824/1‑71 (MQ=255)

                                                            aaTTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAACCGcc       <  1:641104/66‑1 (MQ=255)

                                                             aTTGCTGTACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTcc                           <  1:3550855/45‑1 (MQ=38)

                                                             aTTGCTGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGa                    >  1:444506/1‑52 (MQ=255)

ACCCTGATCGTTAACACCGAGGATGGCGTAAACAATCACCACCAGCATGATGGCCGACAAAATTGCCGGACCAATCCACACCTGCGGTTTCAGCCACTGGCGTTCCTGTTCGATTTCTGAACCGCCCAGGT  >  W3110S.gb/2400213‑2400343

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