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
A25 F66 I1 R1	21	40.5	1611144	86.0%	1385583	142.7

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 subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	97.4%	111.0 / NA	40	P1100Q (CCG→CAG)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (20/18); minor base G (0/1); total (20/20)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATC  >  NC_000913/4184406‑4184679

ggCGGTTAAACGCCGTATACAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                     <  1:772855/143‑1 (MQ=255)

  cttttAAACGCTTTATCCATCCTTGTTACATGATGGCAGGTCGTCACGGCAAGAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATAGTACTGAACCAGCTGGGc                                                                                                                                   <  1:418346/140‑1 (MQ=255)

    gTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGt                                                                                                                                 <  2:331120/143‑1 (MQ=255)

           gCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCACCCCGCTCGAAGATATGCCTTACAATGAAAACGGTACTCCGGTAGAAATAGAACAGAACCAACTGAGCGTACCGtat                                                                                                                          >  1:303383/1‑141 (MQ=255)

                aTCCAGCTTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                     <  1:749156/143‑1 (MQ=255)

                 tCCAGCCGGGTGGCAAGAGGGCAGGTCGCCGCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATg                                                                                                                    <  2:438631/143‑1 (MQ=255)

                   cAGCATGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                  <  1:625663/143‑1 (MQ=255)

                    aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGCTCGAAGATATGCCTTACGCTGCCAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAACGTCTCGTATGAAc                                                                                                                 >  1:196505/1‑143 (MQ=255)

                                  aTGGCAGGTCGTCAGGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                                   <  1:152523/143‑1 (MQ=255)

                                   tGGCAGGTAGTCACGTTAACAAGAGTGTAATTTCTAAGATCAACCCGATCGTAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                  <  2:419486/143‑1 (MQ=255)

                                      cAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGCATGAACATCGGTCAGATCCCCGaa                                                                                               >  2:714935/1‑143 (MQ=255)

                                       aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCTGATCGAAGATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                              <  1:374268/143‑1 (MQ=255)

                                       aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                              <  2:416663/143‑1 (MQ=255)

                                            gtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACACCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAAccccc                                                                                         >  1:704780/1‑141 (MQ=255)

                                               aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCATACTGAACCAGCTGAGCGAACCGTAACTGATGAACATCAGTCAGAACCTCCGAACCCAccag                                                                                      >  1:399076/1‑141 (MQ=255)

                                                       aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAAGAACATCGGTAAGATCCTCGAAACCCACCTGGGTATGGc                                                                              >  1:474099/1‑143 (MQ=255)

                                                        atggTGTAATTTCTAAGATCATCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAATCCACCTGGGTATGGCt                                                                             <  2:712275/141‑1 (MQ=255)

                                                               aaattCTAAGACGAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                      <  2:508520/140‑1 (MQ=255)

                                                                aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCAGCGAACgg                                                                     >  2:656454/1‑143 (MQ=255)

                                                                aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGCCAGATCCTCGAAACCCCCCAGGGAATTGCTGCGCAAgg                                                                     >  2:237417/1‑143 (MQ=255)

                                                                aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTAGTATGAACATCGGTCAGATCCTCGAAACCCACGTGAGAATGGCTGCGaaaca                                                                     >  2:465298/1‑141 (MQ=255)

                                                                     tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGAGCGTACCGTCACGTATGAACATCGGACAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                >  1:462063/1‑143 (MQ=255)

                                                                     tAAGATAAACTCTATCGAAGATATGCCTTACGATGAGAACGGTACGCCGGTAGACATCGTACTGAACCAGCGGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                <  1:520301/143‑1 (MQ=255)

                                                                           cAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACa                                                          >  1:512745/1‑143 (MQ=255)

                                                                            atcgcGATCGAAGGTAGGCGTTACGTGGTGGGCGGTACGCCTGTAGACATCGTACTGAACCGGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                         <  2:343076/139‑1 (MQ=255)

                                                                            aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                         >  1:593576/1‑143 (MQ=255)

                                                                              cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTCCCGTCTCGTCTGAACATCGGTCAGATCCTCGAACCCCACCTGGGTACGGCTGCGAAAGGTATCGGCGACAAGa                                                       >  2:569237/1‑143 (MQ=255)

                                                                                             gCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGCCAAGATCAACGCCATGCTGa                                        >  1:466701/1‑143 (MQ=255)

                                                                                               tttACGATGAAAACGGTACGCCGGTAGACATGGTACTGGCCCAGTGGATCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                      <  1:358829/142‑1 (MQ=255)

                                                                                                ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACCAGATCAACGCCCTGTTGAAAc                                     >  1:163480/1‑143 (MQ=255)

                                                                                                     aTGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcagcag                                <  2:110546/143‑1 (MQ=255)

                                                                                                       gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCAGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACCgccgca                              >  1:258306/1‑143 (MQ=255)

                                                                                                        aaaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCATCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                             >  2:512372/1‑143 (MQ=255)

                                                                                                         aaaCGGTACGCCGGTAGACATCGTACTGGACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGTTGAAACAGCAGCaag                            <  2:333779/143‑1 (MQ=255)

                                                                                                              gTACGCCGGTAGACTTCGTACTTCACCAGCTGGGCGTACCGTCTCGTATGAACTTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAGAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTc                       <  2:8012/143‑1 (MQ=255)

                                                                                                                  gCCGGTGGAGAGCGGACTGAACCAGCGGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                   <  1:476791/143‑1 (MQ=255)

                                                                                                                            aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAACCAGCAGCAAGAAGTCGCGAAACTGCGCGa         >  1:769561/1‑143 (MQ=255)

                                                                                                                               gTACTGACCCTGCTGTTCTTAACTGCTCGTATTAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAtt      <  1:754893/143‑1 (MQ=255)

                                                                                                                               gTACTGAACCAGCTGGGCGTACC‑TCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTAGGTATGGCTGCGAAACGAATCGGCGACAAGATCGAAGACCTGCTGAAACCGCAGCCAGACCACGCGAAACTGCGCGAAttg     >  2:439928/1‑142 (MQ=255)

                                                                                                                                   tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAACCCATc  >  1:502745/1‑143 (MQ=255)

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATC  >  NC_000913/4184406‑4184679

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A