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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,609,336	(C)_7→8	intergenic (+13/‑78)	yjjG → / → prfC	dUMP phosphatase/peptide chain release factor RF‑3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,609,329	1	.	C	94.6%	122.6 / 0.1	37	intergenic (+6/‑85)	yjjG/prfC	dUMP phosphatase/peptide chain release factor RF‑3
Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (18/17); total (19/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

TCGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACTT  >  NC_000913/4609193‑4609459

tcGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑cc                                                                                                                                  <  2:220523/139‑1 (MQ=255)

tcGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑cc                                                                                                                                  <  1:617022/139‑1 (MQ=255)

tcGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑cc                                                                                                                                  >  2:617022/1‑139 (MQ=255)

  ggTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATAGCGAGCAACCAGAAGGCATCGCGCCCACATGGACCGTTTCTTCGTTGCAAGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑cccc                                                                                                                                >  2:1127277/1‑139 (MQ=255)

     ggCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑ccccccc                                                                                                                             >  1:458919/1‑139 (MQ=255)

         tCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGTTTGCCT‑ccccccc                                                                                                                             <  2:880569/135‑1 (MQ=255)

         tCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑ccccccc                                                                                                                             >  1:880569/1‑135 (MQ=255)

          cAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑ccccccccgttg                                                                                                                        <  1:1127277/139‑6 (MQ=255)

             cGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATg                                                                                                                      <  1:216003/139‑1 (MQ=255)

                   gcatGCGACCTCCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTaaa                                                                                                                >  2:763106/4‑139 (MQ=255)

                     ttGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAAt                                                                                                              <  1:835289/139‑1 (MQ=255)

                          aCCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCg                                                                                                         <  2:890964/139‑1 (MQ=255)

                          aCCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCg                                                                                                         >  1:1272039/1‑139 (MQ=255)

                                            cacCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTcaac                                                                                       >  2:34398/1‑139 (MQ=255)

                                                 tCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAACAGCCGCAATTTTTCGTTTTCAACAAgcg                                                                                  >  1:1244624/1‑139 (MQ=255)

                                                         aaCCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGa                                                                          >  2:632621/1‑139 (MQ=255)

                                                          aCCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGAt                                                                         <  1:770159/139‑1 (MQ=255)

                                                           ccAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATg                                                                        >  1:1031982/1‑139 (MQ=255)

                                                                     tCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTc                                                              >  1:555271/1‑139 (MQ=255)

                                                                               cTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGaagaaag                                                    <  2:1031982/139‑1 (MQ=255)

                                                                                      gTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATg                                             <  2:1112719/139‑1 (MQ=255)

                                                                                      gTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATg                                             <  2:1272039/139‑1 (MQ=255)

                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTa                                                                 >  1:178224/1‑118 (MQ=255)

                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTa                                                                 <  2:178224/118‑1 (MQ=255)

                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                            >  2:66126/1‑139 (MQ=255)

                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                            >  1:667468/1‑139 (MQ=255)

                                                                                       tttCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGa                                            >  1:223124/1‑139 (MQ=255)

                                                                                         tcttcGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATTGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACg                                          >  1:514904/1‑139 (MQ=255)

                                                                                               ttGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCt                                                                   <  2:710999/108‑1 (MQ=255)

                                                                                               ttGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCt                                                                   >  1:710999/1‑108 (MQ=255)

                                                                                               ttGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGtct                                    <  2:555271/139‑1 (MQ=255)

                                                                                                 gCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCg                                                                     <  1:66056/104‑1 (MQ=255)

                                                                                                 gCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCg                                                                     >  2:66056/1‑104 (MQ=255)

                                                                                                 gCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGt                                      >  2:679268/1‑135 (MQ=255)

                                                                                                 gCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGt                                      <  1:679268/135‑1 (MQ=255)

                                                                                                        cTGGAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTg                           <  1:34398/139‑1 (MQ=255)

                                                                                                          ggAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCa                         <  2:514904/139‑1 (MQ=255)

                                                                                                          ggAGCAGCTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCa                         <  2:580349/139‑1 (MQ=255)

                                                                                                            agcagcTCCTGTGTAAACACTGATTGCCT‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCaagaag                                                        <  2:992625/105‑1 (MQ=255)

                                                                                                            agcagcTCCTGTGTAAACACTGATTGCCT‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCaagaag                                                        >  1:992625/1‑105 (MQ=255)

                                                                                                                 cTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                       >  2:260442/1‑102 (MQ=255)

                                                                                                                 cTCCTGTGTAAACACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAagaaga                                                       <  1:260442/102‑1 (MQ=255)

                                                                                                                           aaCACTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGcgcc        >  2:248958/1‑139 (MQ=255)

                                                                                                                              acTGATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCa     <  2:223124/139‑1 (MQ=255)

                                                                                                                                 gATTGCCTCCCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACtt  >  1:668482/1‑139 (MQ=255)

TCGGTGGCATCAACGCCGGGCTTGCGACCTGCTGGCTGAATGCACACCATCGCGAGCAACCAGAAGGCATCGCGCCCACCTGGACCGTTTCTTCGTTGCACGAACTGGAGCAGCTCCTGTGTAAACACTGATTGCCT‑CCCCCCCGTTGATGGGTAAAATAGCCGCAATTTTTCGTTTTCAACAAGCGCGGCGCGATGCCGCTTACTCAAGAAGAAAGAATTATGACGTTGTCTCCTTATTTGCAAGAGGTGGCGAAGCGCCGCACTT  >  NC_000913/4609193‑4609459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A