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
A31 F1 I1 R1	21	37.9	2424921	96.5%	2340048	76.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	4,162,513	C→T	T553I (ACT→ATT)	rpoB →	DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	4,162,513	0	C	T	97.1%	122.9 / ‑3.9	34	T553I (ACT→ATT)	rpoB	DNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (18/15); total (18/16)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTC  >  REL606/4162442‑4162582

tATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCAc                                                                   >  2:764660/1‑76 (MQ=255)

     ccGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTAcag                                                              >  2:519148/1‑74 (MQ=255)

     ccGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACgg                                                              >  2:589501/1‑76 (MQ=255)

     ccGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACgg                                                              >  1:829862/1‑76 (MQ=255)

      cGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGTAGTTCGAGACGTACACCCGATTCACTACGGt                                                             >  2:472823/1‑76 (MQ=255)

       gCACTCGGCCCAGGCGGCCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTc                                                            <  1:127820/76‑1 (MQ=255)

           tCGGCCCAGGCGGCCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGt                                                        >  1:81773/1‑76 (MQ=255)

            cGGCCCAGGCGGTCTGACCCGTGAACGCGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCCCTACGGTCGCGTa                                                       >  2:784031/1‑76 (MQ=255)

             ggCCCAGGCGGTCTGACCCGTGAACGTGCAAGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTAGCGTAt                                                      >  1:1105626/1‑76 (MQ=255)

                ccAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTc                                                   <  1:559450/76‑1 (MQ=255)

                  aGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCa                                                 <  1:998680/76‑1 (MQ=255)

                   ggCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCaa                                                >  2:257478/1‑76 (MQ=255)

                    gCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAAt                                               <  1:674629/76‑1 (MQ=255)

                             cccGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAAcccc                                      >  1:801423/1‑76 (MQ=255)

                               cGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTg                                    <  2:683634/76‑1 (MQ=255)

                                gTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGa                                   <  2:635902/76‑1 (MQ=255)

                                gTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGa                                   <  1:221151/76‑1 (MQ=255)

                                       tGCAGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCg                            <  2:1182492/76‑1 (MQ=255)

                                          aGGCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAAc                         >  2:1059422/1‑76 (MQ=255)

                                           ggCTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACa                        <  1:89505/76‑1 (MQ=255)

                                            gCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACAt                       <  1:891453/76‑1 (MQ=255)

                                             cTTCGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATc                      >  2:579542/1‑76 (MQ=255)

                                               tCGAAGTTCGCGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCgg                    >  1:1120361/1‑76 (MQ=255)

                                                cGAAGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGt                   >  1:694155/1‑76 (MQ=255)

                                                 gAAGTTCGACACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTc                  >  2:1041338/1‑76 (MQ=255)

                                                   aGTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTg                <  2:754567/76‑1 (MQ=255)

                                                    gTTCGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGa               <  1:909734/76‑1 (MQ=255)

                                                       cGAGACGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCa            >  2:648551/1‑76 (MQ=255)

                                                        gagaCTTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCaa           >  1:1172598/1‑76 (MQ=255)

                                                           aCGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAActc        <  1:1074276/76‑1 (MQ=255)

                                                            cGTACACCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTNATCAActct       <  1:30131/76‑1 (MQ=255)

                                                              tACACCCGATTCACTACGGTCGCGTATGTGCAATCGTAACCCCTGAAGGTCCGAACANCGGTCTGATCAActctct     <  1:1154489/76‑1 (MQ=255)

                                                               acacCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTg    <  2:449955/76‑1 (MQ=255)

                                                               acacCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTg    >  1:811736/1‑76 (MQ=255)

                                                                 acCCGATTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTc  >  2:713734/1‑76 (MQ=255)

TATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTC  >  REL606/4162442‑4162582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A