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
A4 F111 I2 R1	11	49.6	1720206	93.9%	1615273	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,542	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	4,184,542	0	C	A	95.7%	126.3 / NA	46	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (0/2); new base A (28/16); total (28/18)
Fisher's exact test for biased strand distribution p-value = 1.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184680

tGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTg                                                                                                                                        >  2:203626/1‑143 (MQ=255)

tGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAAAAAGAGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTCCTGAACCAGCTg                                                                                                                                        >  1:395884/1‑143 (MQ=255)

            gCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtat                                                                                                                            >  1:132890/1‑141 (MQ=255)

                   ccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGa                                                                                                                     >  2:70187/1‑143 (MQ=255)

                    cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    >  1:413154/1‑143 (MQ=255)

                    cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    <  1:304720/143‑1 (MQ=255)

                         ttctgtcAAGAGGGCACGTCACAACGGTAACAAGTGGGTAATTGCTAAGATCAACCCGATCCAAGATATGCCCTACGACGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                               <  2:768622/137‑1 (MQ=255)

                             gACAAGATGGTAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                           <  2:19726/143‑1 (MQ=255)

                             gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTCCCGTCCCGTATGAACATCGGTcc                                                                                                           >  1:188653/1‑142 (MQ=255)

                              aCAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTCGACATCGTACTGAACCAGCTGGGCGTACCGTCCCGTATGAACATCGGTCAg                                                                                                          >  2:715260/1‑143 (MQ=255)

                                    tcgCAGCTCGTCACGGTAACAGGGTTGTAATTTCTACGATCGACCCTATCGAAGATATGCCTTACGATGCAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                    <  2:14292/141‑1 (MQ=255)

                                      gCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTGTGAACACCAGTAAGATCCTCGa                                                                                                  >  1:845919/1‑143 (MQ=255)

                                        agtgccgaaCGGGACCAAGGGTGTCGTTTCTAAGATCAGCCCCATCGAAGTTATGCCTTACGAGGAAACCGGTACGCCGGTATACATCGTACTGACCCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                <  2:24957/135‑1 (MQ=255)

                                        aGGGCGTCACGGTAACAAGGGCGTAATCTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGTGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                <  1:464806/143‑1 (MQ=255)

                                           tcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAccc                                                                                             <  1:348262/143‑1 (MQ=255)

                                            cgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAccaa                                                                                            >  2:241756/1‑141 (MQ=255)

                                              tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcc                                                                                          >  2:616407/1‑143 (MQ=255)

                                              tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGGCAGATCCTCGAAAcccccc                                                                                          >  2:465820/1‑143 (MQ=255)

                                                 cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCaagtgg                                                                                       >  2:164158/1‑138 (MQ=255)

                                                           ggTGTAATTTCTAAGATTAACCCGATCGAAGATATTCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATTAACATCTGTCAGATCCTCGAATCCCACCTGGGTATGGCTGc                                                                             <  2:184012/143‑1 (MQ=255)

                                                           ggTGTAATTTCTAAGAAAAACACGATCGAAGATAGGCCGAACGAGGAAAACGGGACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                             <  1:291214/143‑1 (MQ=255)

                                                            gtgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCTGATCCTCGAAACCCACCTGGGTATGGCTGCg                                                                            <  1:107911/143‑1 (MQ=255)

                                                               tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCTTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                         >  1:235278/1‑143 (MQ=255)

                                                                aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                        <  1:76627/143‑1 (MQ=255)

                                                                 aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGAACTAAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAgg                                                                       >  1:460702/1‑143 (MQ=255)

                                                                  tttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGt                                                                      >  1:62111/1‑143 (MQ=255)

                                                                    tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAACCACCTGGGTATGGCTGCGAAAGatat                                                                    >  1:551383/1‑143 (MQ=255)

                                                                      tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTAGAAACCCAGCTGGCGATGGCTGCCAACGGTATCg                                                                  >  2:124025/1‑143 (MQ=255)

                                                                       aaGATCAGCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCgg                                                                 <  2:696987/143‑1 (MQ=255)

                                                                            cAACCCCAGCGAAGATATGCCTTACGAGGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACa                                                            <  2:228459/143‑1 (MQ=255)

                                                                             aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTACGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                           >  2:588575/1‑143 (MQ=255)

                                                                                             tGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTg                                           >  2:36351/1‑143 (MQ=255)

                                                                                               ccTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGGATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaa                                         >  1:253419/1‑143 (MQ=255)

                                                                                                 ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                       >  1:857924/1‑143 (MQ=255)

                                                                                                   aCGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCGGCGAAAGGTATCGGCGACAAGACCAACGCCATGCTGCAagag                                     >  2:275374/1‑143 (MQ=255)

                                                                                                     gATGAAAGCGGTACGCCGGTAGACATAGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTGTCGGCGACAAGACCAACGCCAtccacaaaaaaac                                   >  2:622231/1‑131 (MQ=255)

                                                                                                               gTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCTCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTc                         <  1:360206/143‑1 (MQ=255)

                                                                                                                   gCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGGCGCGa                     >  1:372455/1‑143 (MQ=255)

                                                                                                                      ggTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAAc                  >  1:420069/1‑143 (MQ=255)

                                                                                                                         aGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgc               >  2:434456/1‑143 (MQ=255)

                                                                                                                           aCATCGTACTGAACCACCTGGGCGTACCGTCGCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc             <  2:430437/143‑1 (MQ=255)

                                                                                                                               cGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGGATCGGCGACAAGATCAACGCCATGCTGAAACAGCGGCAAGAAGTCGCGAAACTGCGCGAAt         >  1:54880/1‑143 (MQ=255)

                                                                                                                                gTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCGGCGAAAGGTATCGGCGACCAGACCAACGCCATGGCGAACAAGCAGCAAGAAGCCGCGAAACAGCGCGCAtt        >  2:490754/1‑143 (MQ=255)

                                                                                                                                 tactgtgtccGCTCGGCGTGCCGTCTCGTATGAACATCGGTCAGACCCTCGAAACCCACCTGGGTATGGCTGCGAACGGTATCGGCGACAATATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc       <  1:844231/135‑1 (MQ=255)

                                                                                                                                   gtGAAGCAGCTGGGCTCACCGTCTCGAATGAACATCGGTCAGAGCCACGAAACCCACCTGGGTATGGCTGCGAAAGGAATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCAt     <  1:391445/142‑1 (MQ=255)

                                                                                                                                    tGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCCGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc    <  1:463941/143‑1 (MQ=255)

                                                                                                                                      atcgcGCTGCGCGTGCCGGCTGGTATGACCATCGTTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTATCGGCCACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCa  <  2:654696/139‑1 (MQ=255)

                                                                                                                                      aaCCAGCCGGGCGCACCGCCTCGGATGGACATCGGTCAGGTCCTCGAAACCCACCTGAGTATGGAACTGAAACCGCTAGAGGCCAGTTTCTACGCCATGCTGAAACCGCAGCAATAATGCGCTAAACTGCGCGAATTCATCCa  <  2:608245/143‑1 (MQ=255)

TGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184680

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