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 F108 I1 R1	17	38.6	1469306	86.0%	1263603	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	94.7%	89.0 / NA	40	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (2/0); new base A (15/21); total (18/22)
Fisher's exact test for biased strand distribution p-value = 1.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTC  >  NC_000913/4184406‑4184676

tgCGGTTTAACGCCGTTTCCAGTCTGGTGACAAGATGGTAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                  <  1:485033/142‑1 (MQ=255)

        aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACACCGGAAGACATAGTACTGAAACAGCTGGGCTTAcag                                                                                                                          >  1:1154/1‑141 (MQ=255)

          cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCACCCCGATCGAAGATATGCCTTACGCTGAAAACCGTACGCCGGTGCACATCGTACTGCCCCCGCTCCGCGTCCCGtc                                                                                                                        >  1:76052/1‑143 (MQ=255)

              gTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                    <  2:69555/143‑1 (MQ=255)

               gatgcAGCCGGGGGACAAGAGGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                   <  2:245437/139‑1 (MQ=255)

                    aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGCTGTGCCTTACGCTGAAAACGGTACGCCGGTAGACATCGGACTGAACCTGCTGGGCGTACCGTCTCGTATGAAc                                                                                                              >  1:355561/1‑143 (MQ=255)

                     gCCTGGTGACAAGATGGCAGGTCATCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACCGTCCGACGGTCGACCTCGTCCTGCACCCGCTGGGCGCACCGCCTCCTATGAAcc                                                                                                             >  2:129326/1‑142 (MQ=255)

                                 gctgtgaGGTCGTCACGGTAACAAGGGTGTAATTGCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATcc                                                                                                 <  2:205795/137‑1 (MQ=255)

                                  aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGCACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                                >  1:469234/1‑143 (MQ=255)

                                       agctcctcACGGCAACAAGGGTGTAATTTCTCAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                           <  1:243452/137‑1 (MQ=255)

                                       aGGTCGTCACGGTAACAAGGGGGGAATTTCTAAGATCAACCCGATCGAGTATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                           <  2:114387/143‑1 (MQ=255)

                                         gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGCCTCGTATAAAACTCGGTGAGATCCCCGAAAcc                                                                                         >  2:330595/1‑143 (MQ=255)

                                              cACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAATACGGTACGCTGGTAGTCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCt                                                                                    <  1:67419/143‑1 (MQ=255)

                                               aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGCGCGTACCGTCTCGTATGAACATCGGACAGATCCTCGAAACCCaacag                                                                                   >  1:494186/1‑139 (MQ=255)

                                                 ggTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCACACCGGTCAGATCCTCGAAACCCACCAggg                                                                                 >  1:621601/1‑143 (MQ=255)

                                                  atAACCAGGGTGTAACTGCGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTTCGCCGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGt                                                                                <  2:207291/142‑1 (MQ=255)

                                                    aagaaGGGTGGAATTTCTAAGAGCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTAt                                                                              <  1:703989/140‑1 (MQ=255)

                                                            tgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAACCCACCTGGGGATCGCTGCGa                                                                      >  1:244632/1‑143 (MQ=255)

                                                            tgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGa                                                                      >  1:511917/1‑143 (MQ=255)

                                                              ttaTTTTTAATATCTTCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                    <  1:634549/141‑1 (MQ=255)

                                                               aaTTTCTAAGATCAACCTTATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                   <  1:42700/143‑1 (MQ=255)

                                                               aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCTGTAGACATTGTTTTGGTCGAGCAGAGCGAACCGGCACGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                   <  1:268495/143‑1 (MQ=255)

                                                                 tttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTACGAAAGGt                                                                 >  2:1784/1‑143 (MQ=255)

                                                                   tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCACCTGGGTATAGCTGCAAAAGatat                                                               >  1:680312/1‑143 (MQ=255)

                                                                    cTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCACGGATGAACATCGGTCAGATCCTCGAAACCCACCTCGGTATGGGTGCGAAAGGTATc                                                              >  2:336531/1‑143 (MQ=255)

                                                                     tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGCCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCTGAACCTCGGTCAAATCCTCGAAACCCACCTGGGTATGGCTGCGAAAAGTATCg                                                             >  1:473127/1‑143 (MQ=255)

                                                                     tAAGATCAACCCGATCGAAGATATGCCTTACGAGGAAAACGGTACGCCGGTAGACATCGTACCGAACCAGCCGGGCGTACAGACTCGTATGAACATCGGTCAGGTCCACGAAACCCCCCTCGGTACTGCTGCGAACGGTCTCg                                                             >  2:549395/1‑143 (MQ=255)

                                                                          tCAATCCGATAGAAGATATGCCTTACGATGACAACGGTACGCCGGTAGACATCGTACTGAACTAGCTGTGCGTACCGTCTCCTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                        <  2:205033/143‑1 (MQ=255)

                                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTGAGATCCTCGAAGCCCACCTGGGGATGCCTGCGAAAGGTATCGGCGActa                                                      >  2:373838/1‑141 (MQ=255)

                                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACAAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGagca                                                      >  2:262476/1‑140 (MQ=255)

                                                                               ccGATCGAAGATATGCCTTACGATGAGAACGGTGCGCCGGTAGACATCGTACTGGACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAt                                                   <  2:715147/143‑1 (MQ=255)

                                                                                   tCGAAGATATGCCTTACGATGAAAACGGTACGCTGGTAGACATCGTACTGTACTAGTTGGGCGTAGCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                               <  1:356695/143‑1 (MQ=255)

                                                                                   tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                               <  1:112177/143‑1 (MQ=255)

                                                                                             gCCGTACGATGAAAACGGCACGCCGGTAGACATCGAACTGGACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                     <  2:42846/143‑1 (MQ=255)

                                                                                                               tACGCCGGGAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                   <  2:365935/143‑1 (MQ=255)

                                                                                                                       tAGTCATCGTACGGAACCAGTTGGGTGTACCGTCTCGTATGAACGTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTg           <  2:638324/143‑1 (MQ=255)

                                                                                                                             tcccaCTGACCCGGCTGGGCGTGCCGTCTCGTATGAACAGCGGTCAGATCCTCGAAGCCCGCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa     <  2:621601/139‑1 (MQ=255)

                                                                                                                              cGTACTGAACCAGCTGGGCGTACCGTCTCGTGTGGCCAGCACACAAAGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt    <  1:689874/143‑1 (MQ=255)

                                                                                                                                tACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCACCGCCGTGGGGAAACAGCGGCAAGACGTCGCTCAACTGTGCGAGtta  >  1:3404/1‑142 (MQ=255)

                                                                                                                                caCTGAACCATCTGTGCGTACCGTCTCTTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc  <  1:405329/142‑1 (MQ=255)

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTC  >  NC_000913/4184406‑4184676

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A