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
A14 F1 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,549,037	T→C	V77A (GTC→GCC)	fimH →	minor component of type 1 fimbriae

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,549,037	0	T	C	96.4%	189.1 / ‑2.6	56	V77A (GTC→GCC)	fimH	minor component of type 1 fimbriae
Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (27/27); total (28/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01

CTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGAT  >  NC_000913/4548905‑4549170

cTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACt                                                                                                                                 <  2:992963/139‑1 (MQ=255)

         gTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAgg                                                                                                                        >  2:1211172/1‑139 (MQ=255)

         gTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAgg                                                                                                                        >  1:475153/1‑139 (MQ=255)

                       gTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          <  1:1211172/139‑1 (MQ=255)

                                 aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGc                                                                                                                       <  2:1713099/116‑1 (MQ=255)

                                 aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGc                                                                                                                       >  1:1713099/1‑116 (MQ=255)

                                 aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          <  2:232986/129‑1 (MQ=255)

                                 aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          >  1:232986/1‑129 (MQ=255)

                                     tGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAAt                                                                                            <  1:1012472/139‑1 (MQ=255)

                                      gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAAtt                                                                                           >  1:207133/1‑139 (MQ=255)

                                               gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  <  2:207133/139‑1 (MQ=255)

                                                       ggggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  <  2:309293/131‑1 (MQ=255)

                                                       ggggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  >  1:309293/1‑131 (MQ=255)

                                                        gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  >  2:124184/1‑130 (MQ=255)

                                                        gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  <  1:124184/130‑1 (MQ=255)

                                                         ggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTa                                                                                                               >  1:1591230/1‑100 (MQ=255)

                                                         ggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTa                                                                                                               <  2:1591230/100‑1 (MQ=255)

                                                                   ggTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGt                                                              >  1:772226/1‑139 (MQ=255)

                                                                        tGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTa                                                         >  2:959411/1‑139 (MQ=255)

                                                                         ggATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  <  2:75135/113‑1 (MQ=255)

                                                                         ggATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                                                                  >  1:75135/1‑113 (MQ=255)

                                                                             cTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCAt                                                    <  2:772226/139‑1 (MQ=255)

                                                                               ttCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAAtata                                                                      >  2:171994/1‑119 (MQ=255)

                                                                               ttCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAAtata                                                                      <  1:171994/119‑1 (MQ=255)

                                                                               ttCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCAttt                                                  >  2:325440/1‑139 (MQ=255)

                                                                               ttCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCAttt                                                  >  1:265176/1‑139 (MQ=255)

                                                                                  gACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGc                                                                                                                       <  2:1520890/67‑1 (MQ=255)

                                                                                  gACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGc                                                                                                                       >  1:1520890/1‑67 (MQ=255)

                                                                                  gACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                               <  2:475153/139‑1 (MQ=255)

                                                                                  gACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                               >  1:188756/1‑139 (MQ=255)

                                                                                  gACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                               <  1:870237/139‑1 (MQ=255)

                                                                                       aaaTCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTaccac                                          <  2:265176/139‑1 (MQ=255)

                                                                                         aTCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          >  2:1700580/1‑73 (MQ=255)

                                                                                         aTCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          <  1:1700580/73‑1 (MQ=255)

                                                                                                     aaCGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAAcgccgc                            >  2:1505556/1‑139 (MQ=255)

                                                                                                      aCGATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcg                           <  1:959411/139‑1 (MQ=255)

                                                                                                        gATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcgcg                         <  1:1505556/139‑1 (MQ=255)

                                                                                                        gATTATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcgcg                         <  1:325440/139‑1 (MQ=255)

                                                                                                           tATCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCgttg                      >  2:847902/1‑139 (MQ=255)

                                                                                                            aTCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCgttgt                     >  1:814345/1‑139 (MQ=255)

                                                                                                             tCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcgcg                         <  2:853360/134‑1 (MQ=255)

                                                                                                             tCCGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCcgcgcg                         >  1:853360/1‑134 (MQ=255)

                                                                                                              ccGGAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGttt                   >  2:682726/1‑139 (MQ=255)

                                                                                                                ggAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                               <  1:1344259/109‑1 (MQ=255)

                                                                                                                ggAAACCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCt                                               >  2:1344259/1‑109 (MQ=255)

                                                                                                                  aaaCCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAat                                                                         >  1:1013593/1‑81 (MQ=255)

                                                                                                                  aaaCCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATaa               >  2:928713/1‑139 (MQ=255)

                                                                                                                  aaaCCATTACAGAATATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAat                                                                         <  2:1013593/81‑1 (MQ=255)

                                                                                                                    aCCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGt                                                              >  2:1478094/1‑90 (MQ=255)

                                                                                                                    aCCATTACAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGt                                                              <  1:1478094/90‑1 (MQ=255)

                                                                                                                        ttACAGACTATGCCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          <  2:1452189/42‑1 (MQ=255)

                                                                                                                        ttACAGACTATGCCACACTGCAACGAGGCTCGGCTTATggcg                                                                                                          >  1:1452189/1‑42 (MQ=255)

                                                                                                                          aCAGACTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGaa       <  1:682726/139‑1 (MQ=255)

                                                                                                                              aCTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTgg                                                                  >  2:1248162/1‑76 (MQ=255)

                                                                                                                              aCTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTgg                                                                  <  1:1248162/76‑1 (MQ=255)

                                                                                                                               cTATGCCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGAt  <  2:188756/139‑1 (MQ=255)

CTATTGGCGGTGGCAGCGCCAATGTTTATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTACCACCAGCGAAACGCCGCGCGTTGTTTATAATTCGAGAACGGAT  >  NC_000913/4548905‑4549170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A