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
A8 F110 I1 R1	9	45.0	1568152	94.0%	1474062	142.7

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	98.0%	139.9 / NA	51	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (23/26); total (25/26)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184403‑4184680

cTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGcc                                                                                                                                         >  2:64131/1‑142 (MQ=255)

  ggCGGTTAAGCGCTGTATCTAGTCTGGTGACAAGAGGGCAGCTCGTCCCGGTAACAAGGGTGTAATTTCTAAGAGGAGCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                       <  1:512618/143‑1 (MQ=255)

     ggTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCg                                                                                                                                    >  1:255730/1‑143 (MQ=255)

     ggTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGCTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGCACCAGCTGGGCg                                                                                                                                    >  2:530761/1‑143 (MQ=255)

        tAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCGGCTGGGCGTAc                                                                                                                                 >  1:128364/1‑143 (MQ=255)

        gaaaCGCCGTATCCAGCCTGGTGACAAGAGGGCAGGGCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAc                                                                                                                                 <  2:728147/142‑1 (MQ=255)

           aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGAGCGTACCGt                                                                                                                              >  2:40109/1‑143 (MQ=255)

               cGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTGAGATCACCCCGATGGAAGATATGCCGTGCGATGAAACACGTACGCCGCTAGACATCGCACAGAACACGCTGGGCGTAcggcatcg                                                                                                                          >  1:680708/1‑136 (MQ=255)

                  aTCCAGTCTGGTGACAAGATGGCAGGTCGTCACGGGAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                       <  2:162579/143‑1 (MQ=255)

                  aTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAACTGGGCGTAACGTCTCGTAt                                                                                                                       >  2:182927/1‑143 (MQ=255)

                   tCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTagg                                                                                                                      >  1:44189/1‑141 (MQ=255)

                     cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCACCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    <  1:624759/143‑1 (MQ=255)

                     cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    >  2:64123/1‑143 (MQ=255)

                         ctagTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATc                                                                                                                >  2:749494/4‑143 (MQ=255)

                         cTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAACCTAACGCCAATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATc                                                                                                                <  1:177734/143‑1 (MQ=255)

                              gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                           <  1:739152/143‑1 (MQ=255)

                              gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                           >  1:762348/1‑143 (MQ=255)

                                 aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                                        >  1:3075/1‑143 (MQ=255)

                                 aaGAGGGCAGGTCGGCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                                        <  1:704841/143‑1 (MQ=255)

                                                      aaCCAGGGTGTAATTTCGAAGAGCAACCCGATCGAAGATATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTAt                                                                                   <  2:405252/143‑1 (MQ=255)

                                                            ggTGGAATTACGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                             <  1:282559/143‑1 (MQ=255)

                                                                tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                         >  1:512130/1‑143 (MQ=255)

                                                                  aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAgg                                                                       >  1:190772/1‑143 (MQ=255)

                                                                       tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCATCTGGGCGTACCGTCTCGTATGAACATCGATCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                  >  1:445111/1‑143 (MQ=255)

                                                                            tCATCCCGATCGAGGCTATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGGAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGAc                                                             <  2:584135/143‑1 (MQ=255)

                                                                            tCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTAACGGCGAc                                                             >  2:222403/1‑143 (MQ=255)

                                                                             cAACCCGGTGGCAGATATGCCTTACGATGAAACCGGTACGCCGGTAGACATCTTACTGAACCAGCTGGGCGTACCGTCTCGTTTGAAGTTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACa                                                            <  1:111225/143‑1 (MQ=255)

                                                                              aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                           <  1:152408/143‑1 (MQ=255)

                                                                              aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGCAAGATCCTGCACACCCTGCTGGGTATGGCTGCGAAAGGTCTCGGCGCCac                                                           >  2:757407/1‑142 (MQ=255)

                                                                                cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAgg                                                         >  1:256054/1‑142 (MQ=255)

                                                                                  cGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATc                                                       >  1:551632/1‑143 (MQ=255)

                                                                                         aGATATGCCTTACGAGCAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCa                                                <  2:484804/143‑1 (MQ=255)

                                                                                         aGATATGCCTTACGACGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCa                                                <  1:380761/143‑1 (MQ=255)

                                                                                           atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGCCAAGATCAACGCCATg                                              >  1:651790/1‑143 (MQ=255)

                                                                                                ccTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaa                                         >  2:323150/1‑143 (MQ=255)

                                                                                                 cTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                        <  1:213893/143‑1 (MQ=255)

                                                                                                  ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                       <  1:522757/143‑1 (MQ=255)

                                                                                                    aCGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcag                                     <  1:738123/143‑1 (MQ=255)

                                                                                                         gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGAATGGCTGCGAAAGGTAGCGGCGACAAGATCAACGCCATGATGAAACGgcagca                                >  2:617153/1‑143 (MQ=255)

                                                                                                           aaaCGGTACGCCGGTAGACATCGTCCTGACCCAGCTGGGCGTACCGTCTCGTAGGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaag                              <  1:756595/143‑1 (MQ=255)

                                                                                                            aaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTATCGGCGACCGGATCAACGCCATGCTGAAACAGCAGCcaga                             >  2:295781/1‑143 (MQ=255)

                                                                                                            aaCGGTACGCCGGTAGACATCGTACGGAACCAACGGGGAGAACCATCACGTGTGAAAATCGGCCAGAAACTCCAAACCCACCCGGGTAGAGATGGGAAAGGTAACAGCGACCAGATGAACGCCTAACTGACACAGCAGCaaga                             >  2:393993/1‑143 (MQ=255)

                                                                                                               ggTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaagttgt                          <  2:135533/143‑5 (MQ=255)

                                                                                                                    gCCGGTAGACCTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCGCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATTCTGAAACAGCAGCAAGAAGTCGCGa                     <  1:493909/143‑1 (MQ=255)

                                                                                                                            aCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc             <  1:526742/143‑1 (MQ=255)

                                                                                                                            aCATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc             <  1:749494/143‑1 (MQ=255)

                                                                                                                                ctgaCTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAGCCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt         <  1:353509/140‑1 (MQ=255)

                                                                                                                                   acggAACCAGCTGGGCGCACCGGCTCGCATTACCACCGGTCGAATCCGCGAAACCCACCGGGGTAGGGCTGCGAAATGTATCGGCGACAAGATCAACGCCATGCCGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCa      <  2:354464/140‑1 (MQ=255)

                                                                                                                                     tGAACCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGGAGCAAGAAGTCGCGAAACTGCGCGAATTCATc    <  1:53639/143‑1 (MQ=255)

                                                                                                                                       aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCa  <  2:255730/143‑1 (MQ=255)

                                                                                                                                       aaCCAGCTGGGCGTACCGTCTAGTATGAACATCGGACAGATCGGCGAAACCAACCTGGGTATGGCTGCGAAAGGTGTCGGCGACAGGAGCAAGGCCATGCTGAAAAAGCAGAAAGAAGCCGAGAAACTGCGCGaactgaacaa  >  2:282205/1‑135 (MQ=255)

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184403‑4184680

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