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
A21 F59 I1 R1	23	54.9	2144786	90.8%	1947465	141.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	461,010	C→A	T708N (ACT→AAT)	lon →	Lon protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	461,010	0	C	A	97.4%	110.0 / NA	39	T708N (ACT→AAT)	lon	Lon protease
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (21/16); minor base G (0/1); total (21/18)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GACATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGAT  >  NC_000913/460874‑461149

gACATCCACGTCCACGTACCGGCAGGCGCGCCGCCGCCAGATGGTCAGAGTGCCGGTATTGCCATATGCACAGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGCGCTCAATCTGCg                                                                                                                                       >  1:181014/1‑143 (MQ=255)

 gcagccacggccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGt                                                                                                                                      <  2:941005/139‑1 (MQ=255)

 aCATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGATTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGt                                                                                                                                      <  2:933300/143‑1 (MQ=255)

         gtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGAACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGCTCGATCTGCGTGGTCAGGt                                                                                                                              >  1:798301/1‑143 (MQ=255)

                      caGGTGCGCCGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGCCCGGTAGCCCGGTTCGTGCCGATGTGGCAATGACCGGAGCATCCTATCTACGTGGTCAGGTACTGCCGATCggt                                                                                                                 <  2:231996/142‑1 (MQ=255)

                         gTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCggtggt                                                                                                              >  1:599937/1‑143 (MQ=255)

                              tcgcgcaaaGATGGTCCGGGCGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTgaa                                                                                                         <  2:106521/137‑1 (MQ=255)

                              aCGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGGACGGTACGCCGGTTCGTGCCGGTGTGGCAATGACCGCTGTGATCAGGCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTgaa                                                                                                         <  2:181014/143‑1 (MQ=255)

                               cGCCGAAAGATGGTCCGAGTGCCGGTAGTGCTATGTGCACCGCGCTGGTGTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTgaaa                                                                                                        <  2:958098/143‑1 (MQ=255)

                                 ccGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCCATCTGCGTGGTCAGGTCCTGCCGATCGGTGGTTTgaaaga                                                                                                      >  1:898027/1‑143 (MQ=255)

                                   gcaaGACGGGCCGGGGGCCGGTAGTGCTATGTGCACCGCGCTGGTGTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTgaaagaaa                                                                                                    <  2:145020/141‑1 (MQ=255)

                                     gaGATGGTCCGAGTGCCGGTCTTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCTGTTGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGaaaaa                                                                                                  <  1:149926/142‑1 (MQ=255)

                                     aaGATGGTCCGACTGCCGGTATTGCTATGTTCACCGCTCTGGTTTCTTGCCTGACCGGTAACCCTGTTCGTGCCCATATCCCAATTACCGGTGACATCAATCCGCGTCGTCACGTACTGCCGATCTGTCGTTTGAAATaaaaa                                                                                                  <  1:737975/143‑1 (MQ=255)

                                            tCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTgg                                                                                           >  2:252007/1‑143 (MQ=255)

                                              cGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTGTGCAAGAAAAACTCCTGGCa                                                                                         >  1:364989/1‑143 (MQ=255)

                                               gcgTGCCGGTACTGCTATGTGGACCGCGCTGGTTTCCTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAg                                                                                        <  2:303467/141‑1 (MQ=255)

                                                tttGCCCGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAgc                                                                                       <  2:57143/141‑1 (MQ=255)

                                                            gctcagtgCCCCGCGGGTGTTTCTTGCCTGGCCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGcggcgg                                                                           <  1:945834/138‑1 (MQ=255)

                                                            gCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGcggcgg                                                                           <  1:346335/143‑1 (MQ=255)

                                                                 gtgCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGGTTa                                                                      >  1:897833/1‑143 (MQ=255)

                                                                   gCAGCGCGCTGGTTTGATCCCGGACGGGGTTCCCGGTGGGGGCCGATGTGGCAACGACGGGGGGGATCAATCTGCGTGGGCAGGTACTGCCGATCGGCGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTaaa                                                                    <  2:216774/143‑1 (MQ=255)

                                                                    cACCGCGATGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTaaaa                                                                   <  2:855278/143‑1 (MQ=255)

                                                                      ccGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCCTCGCGGCGGGATTacaaca                                                                 >  2:487885/1‑143 (MQ=255)

                                                                           cTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCt                                                            >  1:1028280/1‑143 (MQ=255)

                                                                               tttCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGGTTGCAAGAACAACTCCTGGCCGTGCATCGCGGCGGGAGTAAACCAGTGCTCAtg                                                        >  2:522315/1‑142 (MQ=255)

                                                                                ttCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAAGTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTc                                                       >  2:112387/1‑143 (MQ=255)

                                                                                   ttGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTACTTCCGt                                                    >  1:168970/1‑143 (MQ=255)

                                                                                              gTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATaac                                         >  1:798699/1‑142 (MQ=255)

                                                                                                  cccGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAAcgcg                                     >  1:169904/1‑143 (MQ=255)

                                                                                                   ccGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGa                                    >  2:673168/1‑143 (MQ=255)

                                                                                                     ggTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATc                                  <  1:673168/143‑1 (MQ=255)

                                                                                                     ggTTCGTGCCGATGTGGCAATGACCCGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATc                                  <  2:269438/143‑1 (MQ=255)

                                                                                                                        aTGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGGTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACCGTGCTACTTCCGTTCGAAAATAAACGCGATCTGGAAGAGATCCCTGAcca               >  1:417142/1‑141 (MQ=255)

                                                                                                                                 gagaTCATTCGTCGGGGTCAGGTACTGCCGCGTGGTGGTTGGAGAGAAAAACTCGTGGCAGCGCATCGCGGCGGGAGTAAAGCAGTGCTAATGCCGTTCGACAATAAGCGCGATCTGGAAGAGATTCCTGACAACGTAATTGc      <  2:299843/143‑1 (MQ=255)

                                                                                                                                  agaTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATCCATGACCATGTACTTGcc     >  1:140808/1‑143 (MQ=255)

                                                                                                                                    aTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATCAACGCGATCTGGAAGAGATTCCTGGCAACGTAATTGCCGa   >  2:772090/1‑143 (MQ=255)

                                                                                                                                    aTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTGCTGACAACGTAATTGCCGa   >  1:178255/1‑143 (MQ=255)

                                                                                                                                    aTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGa   >  1:812948/1‑143 (MQ=255)

                                                                                                                                     tCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAGACAGTGCTAATTGCGTTCGAAAATAGACGCGATCTGGAAGACATTCCTGGCACCGTAATTGCCggg  >  2:1006654/1‑141 (MQ=255)

GACATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGAT  >  NC_000913/460874‑461149

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