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 F2 I228 R1	214	26.5	1448192	97.1%	1406194	86.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	386,045	T→C	pseudogene (339/1527 nt)	BW25113_RS01915 →	outer membrane autotransporter barrel domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	386,045	0	T	C	93.5%	87.5 / ‑1.1	31	pseudogene (339/1527 nt)	BW25113_RS01915	outer membrane autotransporter barrel domain‑containing protein
Reads supporting (aligned to +/- strand): ref base T (2/0); new base C (16/13); total (18/13)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.04e-01

GCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACT  >  NZ_CP009273/385960‑386129

gCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGa                                                                                  >  1:626622/1‑90 (MQ=255)

  aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                                <  1:675554/90‑1 (MQ=255)

  aCGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGAtt                                                                                <  1:513078/90‑1 (MQ=255)

            ccTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgc                                                                      <  1:113944/90‑1 (MQ=255)

               attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgcttc                                                                   >  1:330997/1‑88 (MQ=255)

               attattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTAtgctgc                                                                   >  2:10452/1‑90 (MQ=255)

                ttattTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGcc                                                                  >  2:663902/1‑90 (MQ=255)

                    ttGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTATTTCTATGCTGCCTGGc                                                              <  1:546327/90‑1 (MQ=255)

                                      gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTATTTCTATCCTCCCTGGCGGTTATTATGATCGtttt                                            >  1:383835/1‑90 (MQ=255)

                                      gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGtttt                                            >  1:559271/1‑90 (MQ=255)

                                      gACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGtttt                                            >  1:659635/1‑90 (MQ=255)

                                          gTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATg                                        >  2:82791/1‑90 (MQ=255)

                                           tACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                       <  2:260157/90‑1 (MQ=255)

                                           tACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                       <  1:464225/90‑1 (MQ=255)

                                               gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   >  2:539074/1‑90 (MQ=255)

                                               gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  1:381039/90‑1 (MQ=255)

                                               gCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGAt                                   <  1:663902/90‑1 (MQ=255)

                                                  aaTCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGt                                >  2:63229/1‑90 (MQ=255)

                                                             tatCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTggg                     <  1:248578/90‑1 (MQ=255)

                                                                 aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                       <  2:142675/68‑1 (MQ=255)

                                                                 aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGc                                       >  1:142675/1‑68 (MQ=255)

                                                                 aGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGa                 >  2:58164/1‑90 (MQ=255)

                                                                     aTTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             >  2:34565/1‑90 (MQ=255)

                                                                     aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  2:659635/90‑1 (MQ=255)

                                                                     aTTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATg             <  1:15522/90‑1 (MQ=255)

                                                                          gTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGAtttt        >  1:578222/1‑90 (MQ=255)

                                                                          gTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTGTGGTCGTTTTGATGCAGATGGTAATAATCTGGGGGGATATGAtttt        >  1:320026/1‑90 (MQ=255)

                                                                               tCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTacac   <  2:432389/90‑1 (MQ=255)

                                                                               tCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTacac   >  1:204217/1‑90 (MQ=255)

                                                                               tCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAAAAATCTGGGGGGGTATGATTTTTacac   >  1:174544/1‑90 (MQ=255)

                                                                                cACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGATGGGAATAATCTGGGGGGATATGATTTTTACACt  >  1:453462/1‑90 (MQ=255)

GCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACT  >  NZ_CP009273/385960‑386129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

ACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACTGATG  >  NZ_CP009273/385950‑386133

ACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGA                                                                                      >  SRR3722112.636301/1‑100 (MQ=60)

            ACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                                          <  SRR3722112.686109/100‑1 (MQ=60)

            ACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGC                                                                          <  SRR3722112.520585/100‑1 (MQ=60)

               ATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTTC                                                                       >  SRR3722112.334987/1‑100 (MQ=60)

                      CCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGG                                                                <  SRR3722112.115357/100‑1 (MQ=60)

                              TTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTATTTCTATGCTGCCTGGCGGTTATTATG                                                        <  SRR3722112.554544/100‑1 (MQ=60)

                                      TGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTATTTCTATCCTCCCTGGCGGTTATTATGATCGTTTT                                                >  SRR3722112.388824/1‑100 (MQ=60)

                                      TGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTTTTTTGATCGTTTT                                                >  SRR3722112.669928/1‑100 (MQ=60)

                                      TGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTT                                                >  SRR3722112.567752/1‑100 (MQ=60)

                                               AGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGGTTACTTCTATTCTGCCTTGCGGTTATTATGATCGTTTTtatgatgat                                       >  SRR3722112.87977/1‑91 (MQ=60)

                                                     TACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAAT                                 <  SRR3722112.470817/100‑1 (MQ=60)

                                                         GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC                             <  SRR3722112.385988/100‑1 (MQ=60)

                                                         GCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATC                             <  SRR3722112.674258/100‑1 (MQ=60)

                                                                 GCTTGATATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGgaatctgtctcttata                     >  SRR3722112.144460/1‑84 (MQ=60)

                                                                       TATCAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGAT               <  SRR3722112.251518/100‑1 (MQ=60)

                                                                          CAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTT            >  SRR3722112.587049/1‑100 (MQ=60)

                                                                          CAGTAATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTGTGGTCGTTTTGATGCAGATGGTAATAATCTGGGGGGATATGATTTT            >  SRR3722112.323769/1‑100 (MQ=60)

                                                                               ATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACAC       <  SRR3722112.15717/100‑1 (MQ=60)

                                                                               ATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGGGGGTATGATTTTTACAC       >  SRR3722112.206695/1‑100 (MQ=60)

                                                                               ATTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAAAAATCTGGGGGGGTATGATTTTTACAC       >  SRR3722112.176681/1‑100 (MQ=60)

                                                                                TTCAGTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGGTATTATGATCGTTTTGATGCAGATGGGAATAATCTGGGGGGATATGATTTTTACACT      >  SRR3722112.459833/1‑100 (MQ=60)

                                                                                    GTGATTCACGGCTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTTATGCAGATGGTAATAATCTGGGGGGATATGATTTTTTCACTGATG  >  SRR3722112.690616/1‑100 (MQ=60)

ACCGTTAACGGCACGATCTCAACCTATTATTTGAACCATGATTATGCAGACAGTACTGCTAATCAGCTTGATATCAGTAATTCAGTGATTCACGGTTCGATTACTTCTATGCTGCCTGGCGGTTATTATGATCGTTTTGATGCAGATGGTAATAATCTGGGTGGATATGATTTTTACACTGATG  >  NZ_CP009273/385950‑386133

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 7 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`