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
A11 F1 I2 R1	59	52.6	2411032	94.1%	2268781	113.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,561,426	(G)_5→6	coding (27/831 nt)	glpG ←	rhomboid intramembrane serine protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,561,421	1	.	G	97.6%	149.5 / ‑3.2	41	coding (32/831 nt)	glpG	rhomboid intramembrane serine protease
Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (21/19); total (22/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.25e-01

AAAACGCGCCAGCTCCGCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGC‑GGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCGGGAAACTGACGTTGCCAGGCTTCAAAGCCGC  >  NC_000913/3561288‑3561552

aaaaCGCGCCAGCTCCGCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGC‑ggggg                                                                                                                                <  1:227613/139‑1 (MQ=255)

        ccAGCTCCGCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCaa                                                                                                                         <  2:629735/139‑1 (MQ=255)

           gCTCCGCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAag                                                                                                                      <  2:291598/139‑1 (MQ=255)

                gCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTa                                                                                                                 <  2:484434/139‑1 (MQ=255)

                gCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTa                                                                                                                 <  2:930095/139‑1 (MQ=255)

                      aCGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAatcatc                                                                                                           >  1:627779/1‑139 (MQ=255)

                      aCGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGC‑ggggggtt                                                                                                                             >  1:865547/1‑117 (MQ=255)

                      aCGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTCGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGC‑ggggggtt                                                                                                                             <  2:865547/120‑4 (MQ=255)

                       cgcgCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAAtcatca                                                                                                          >  2:164462/1‑139 (MQ=255)

                                  tGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCt                                                                                               <  1:142902/139‑1 (MQ=255)

                                  tGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCt                                                                                               <  1:164462/139‑1 (MQ=255)

                                  tGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCt                                                                                               <  2:339501/139‑1 (MQ=255)

                                       cTCATCATCCAGCCAAACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGTAAAAGAGGTAATCATCAAAATCGTTGCTGTCGc                                                                                          <  2:582925/139‑1 (MQ=255)

                                          aTCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTa                                                                                                                 >  2:714/1‑113 (MQ=255)

                                          aTCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTa                                                                                                                 <  1:714/113‑1 (MQ=255)

                                          aTCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTa                                                                                       >  2:504993/1‑139 (MQ=255)

                                                          tCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAgggg                                                                       <  1:504993/139‑1 (MQ=255)

                                                           cGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGa                                                                      <  1:6149/139‑1 (MQ=255)

                                                           cGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGa                                                                      <  2:627779/139‑1 (MQ=255)

                                                             cTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACa                                                                    >  2:107792/1‑139 (MQ=255)

                                                                  gTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGAc                                                                     >  1:625879/1‑133 (MQ=255)

                                                                  gTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGAc                                                                     <  2:625879/133‑1 (MQ=255)

                                                                     aTGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAg                                                            >  1:656020/1‑139 (MQ=255)

                                                                            tgAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTAcg                                                     >  2:770216/1‑139 (MQ=255)

                                                                            tgAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTAcg                                                     >  2:1188054/1‑139 (MQ=255)

                                                                             gAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTa                                                                                                                 >  1:970834/1‑78 (MQ=255)

                                                                             gAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTa                                                                                                                 <  2:970834/78‑1 (MQ=255)

                                                                             gAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTAcgc                                                    >  2:1028511/1‑139 (MQ=255)

                                                                                tCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGcc                                                 >  1:502862/1‑139 (MQ=255)

                                                                                   tGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGa                                                                      >  1:927136/1‑115 (MQ=255)

                                                                                   tGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGa                                                                      <  2:927136/115‑1 (MQ=255)

                                                                                        aTAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCa                                         >  1:1111269/1‑139 (MQ=255)

                                                                                          aaCACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCAcc                                       >  2:1161571/1‑139 (MQ=255)

                                                                                                cTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCg                                 <  1:1028511/139‑1 (MQ=255)

                                                                                                 tGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATc                                                                                                     >  2:262432/1‑70 (MQ=255)

                                                                                                 tGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATc                                                                                                     <  1:262432/70‑1 (MQ=255)

                                                                                                 tGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCgg                                >  2:1062435/1‑139 (MQ=255)

                                                                                                 tGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCgg                                >  1:865355/1‑139 (MQ=255)

                                                                                                         cATGTAATCAACAAACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCGGGAAACTGa                        <  1:1188054/139‑1 (MQ=255)

                                                                                                                   acaaACGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCGGGAAACTGACGTTGCCAgg              >  2:185391/1‑139 (MQ=255)

                                                                                                                     aaaCGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACgcgc                                                  >  2:1125692/1‑101 (MQ=255)

                                                                                                                     aaaCGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACgcgc                                                  <  1:1125692/101‑1 (MQ=255)

                                                                                                                       aCGCCTGCGCCACGCGGGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCGGGAAACTGACGTTGCCAGGCTTc          >  2:194095/1‑139 (MQ=255)

                                                                                                                              cgcCACGC‑GGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCGGGAAACTGACGTTGCCAGGCTTCAAAgccgc  >  2:467745/1‑139 (MQ=255)

AAAACGCGCCAGCTCCGCCCGTACGCGCTCGGCCTGGGACTCATCCGCCAGCCAGACATCGCTTTGGTTATGTTGTTGAATCGTGAGGATAACACCCTGCGTCGCCATGTAATCAACAAACGCCTGCGCCACGC‑GGGGGTTAGCAAAAGAGGTAATCATCAACATCGTTGCTGTCGCTTATTCCACACAAAAGGGGACAGTATAAAGCGTTACGCGCCGTACGCCACCTCTGCGGGAAACTGACGTTGCCAGGCTTCAAAGCCGC  >  NC_000913/3561288‑3561552

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A