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
A6 F110 I1 R1	11	49.5	1781824	94.3%	1680260	142.4

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	97.7%	126.5 / NA	43	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (26/16); minor base G (0/1); total (26/17)
Fisher's exact test for biased strand distribution p-value = 3.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCC  >  NC_000913/4184410‑4184679

ttAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTa                                                                                                                                 >  1:120481/1‑143 (MQ=255)

    aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGt                                                                                                                             <  1:152319/143‑1 (MQ=255)

      gCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACACCGGACTGAACCAGCTGGGCGGACCGtct                                                                                                                           >  2:887346/1‑143 (MQ=255)

      gCCGTATCCAGCCTGGTGACAAGATAGCAGGTCGACACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGACGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGACGGGCCGACCGtct                                                                                                                           >  1:233656/1‑143 (MQ=255)

         gTATCCAGCCTGTTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                        <  2:402456/143‑1 (MQ=255)

              cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCTGaa                                                                                                                   >  2:443022/1‑143 (MQ=255)

              cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATAGGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                   >  2:758032/1‑143 (MQ=255)

                 ccTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAt                                                                                                                >  2:490162/1‑143 (MQ=255)

                   tGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                              >  2:68147/1‑143 (MQ=255)

                   tGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                              <  1:372409/143‑1 (MQ=255)

                   tGGCGACAACAGGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                              <  1:279162/143‑1 (MQ=255)

                   gttttaCAAGATGGCAGGTCGTTACGGTAACAGGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGGTGAAAACGGTACGCCGGTAGACTTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                              <  1:282938/138‑1 (MQ=255)

                           acagggCACGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCTTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATc                                                                                                      <  2:539239/139‑1 (MQ=255)

                                        tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcc                                                                                         >  2:278553/1‑143 (MQ=255)

                                            ggTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                                     >  2:565875/1‑143 (MQ=255)

                                                 cgaGGGTGGAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                                <  2:856298/141‑1 (MQ=255)

                                                 cAAGGGCGTCATTGCTAAGAGCAGCCCGGTCGAAGATATGCCGGACGATGGAAACGGTACGCCGGTAGACATCGTACTGAACCATCTGGGCGTACCGTCTCGTATGAGCATCGGTCAGAGCCTCGAAACCCACCTGGGTATgg                                                                                <  1:792476/143‑1 (MQ=255)

                                                     ggtggcaatgcTAAGCTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCCCGAAACCCACCTGGGTATGGCTGc                                                                            <  2:624455/133‑1 (MQ=255)

                                                      gtgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTATGGCTGCg                                                                           >  1:14297/1‑143 (MQ=255)

                                                       tgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTCCTGAACCAGCTGGGCGTACCGTCCCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGCATGGCTGCGa                                                                          >  2:305909/1‑143 (MQ=255)

                                                        gtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaa                                                                         >  2:561196/1‑143 (MQ=255)

                                                         tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGgaa                                                                        >  2:803521/1‑143 (MQ=255)

                                                                tAAGATCAACCCGATCGAAGATATGCCTTACGACGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCGGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                 <  2:120481/143‑1 (MQ=255)

                                                                ggagagCAGCCCGATCGATTAGCTGCCGCACGTTGAGAACGCTACGCCGGTAGACATCGTACTGATCCAGCTGGGCGTACCGGCTCGTATGAAGATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                 <  1:792203/141‑1 (MQ=255)

                                                                  aGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATACTCGACACCCAACTGGGGACAGCGGGGAAAGGTacaggc                                                               >  1:780454/1‑138 (MQ=255)

                                                                       acccccaccgcaGATATGCGGTACGATGAACACCGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                          <  2:550016/132‑1 (MQ=255)

                                                                       aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGAGCGTACCGTCTCGTGTGAACATCCGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGCAAGGTATCTGCGACaa                                                          >  2:124596/1‑143 (MQ=255)

                                                                            gATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCa                                                     <  2:353662/143‑1 (MQ=255)

                                                                              tCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                   <  1:763230/143‑1 (MQ=255)

                                                                                  cggtgggCCTTGCGATGAAACCGGTACGCGGGTCGACATGGTACTGAACCGGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCa                                               <  1:25358/137‑1 (MQ=255)

                                                                                          ctgaCGGTGAAAGCGGTACGCCGGTAGGCGTCGTACTGAACGAGCTGGGCGTATCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                       <  1:216823/140‑1 (MQ=255)

                                                                                           ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                      >  1:696688/1‑143 (MQ=255)

                                                                                           ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                      >  2:859195/1‑143 (MQ=255)

                                                                                           ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                      >  1:324194/1‑143 (MQ=255)

                                                                                           ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCCCGAAACCCACCTGGGTATGGCTCCGAAAGGTATCAACGACAAGATCAAAGCCAAGCTGAAAc                                      >  2:149460/1‑143 (MQ=255)

                                                                                                  gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAgcagca                               >  2:701730/1‑143 (MQ=255)

                                                                                                    aaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGGAAGGGATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaag                             >  2:49955/1‑143 (MQ=255)

                                                                                                        ggTACGCCGGTAGACATCGTACTGAACCAGCAGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCAGGGTATGGCTGCGAAAGGTATCGGCGACAAGAACAACGCCATGCGGAAACAGCAGCaagaaaa                         >  1:37918/1‑141 (MQ=255)

                                                                                                            cGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGACTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCCGCGAAAGGGATCGGCGACCAGGTCAGCGCCATGCGGAAACAGCAGCAAGGAGGcgcg                     >  1:119690/1‑143 (MQ=255)

                                                                                                             gCCGGTAGACATCGTACTGAAACAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCCTGCTGACACAGCagaaagaaacagcga                    >  1:136027/1‑136 (MQ=255)

                                                                                                                        tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGACAACAACCTGTGTATGGCTGCGAAAGGTATCCGCGACAAGACCAACGCCCTGCTGAAACAGCAGCCAGAAGTCGCGACACTCCGCGac         >  1:821418/1‑142 (MQ=255)

                                                                                                                        tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa         <  2:562982/143‑1 (MQ=255)

                                                                                                                               gAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATcc  >  2:386805/1‑143 (MQ=255)

TTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCC  >  NC_000913/4184410‑4184679

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