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	1,511,099	G→A	R366H (CGC→CAC)	ydcR →	putative DNA‑binding transcriptional regulator and putative aminotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,511,099	0	G	A	94.1%	154.1 / 1.6	51	R366H (CGC→CAC)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
Reads supporting (aligned to +/- strand): ref base G (1/2); new base A (26/22); total (27/24)
Fisher's exact test for biased strand distribution p-value = 5.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.34e-01

GGTTGGGTCGCCGCCGGAAAACATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCGCCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAGTGGTTACTTTCTCTGGTTGGA  >  NC_000913/1510963‑1511213

ggttggGTCGCCGCCGGAAAACATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCAcc                                                                                                                  >  1:561000/1‑139 (MQ=255)

      gTCGCCGCCGGAAAACATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCACCGATACGACGCCCATCTTCGTCACCTGCGTc                                                                                                            >  2:1096370/1‑139 (MQ=255)

           cgccgGAAAACATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAg                                                                                                       >  2:1054748/1‑139 (MQ=255)

                gAAAACATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCACCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGc                                                                                                  <  1:1096370/139‑1 (MQ=255)

                  aaaCATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCgg                                                                                                <  2:1082041/139‑1 (MQ=255)

                  aaaCATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCgg                                                                                                <  1:1054748/139‑1 (MQ=255)

                         cACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTaa                                                                                         >  1:91144/1‑139 (MQ=255)

                               aaaTTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACg                                                                                   >  1:131424/1‑139 (MQ=255)

                                       cGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTggc                                                                           >  2:517946/1‑139 (MQ=255)

                                       cGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTggc                                                                           <  1:434944/139‑1 (MQ=255)

                                          ttGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTggcagg                                                                        >  2:689499/1‑139 (MQ=255)

                                           tGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTggcaggc                                                                       >  2:12587/1‑139 (MQ=255)

                                            gCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTa                                                                                          >  2:371451/1‑119 (MQ=255)

                                            gCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTa                                                                                          <  1:371451/119‑1 (MQ=255)

                                              aGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCGCCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCAct                                                                    <  2:982165/139‑1 (MQ=255)

                                              aGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCAct                                                                    <  1:1120043/139‑1 (MQ=255)

                                                  gatgaGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCActgctg                                                                <  1:916584/139‑1 (MQ=255)

                                                    tgaGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCg                                                              >  1:221374/1‑139 (MQ=255)

                                                        tACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTAt                                                          >  1:1196482/1‑139 (MQ=255)

                                                          cGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTa                                                           >  2:246214/1‑136 (MQ=255)

                                                          cGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTa                                                           <  1:246214/136‑1 (MQ=255)

                                                               tCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGcc                                                                               >  2:569958/1‑111 (MQ=255)

                                                               tCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGcc                                                                               <  1:569958/111‑1 (MQ=255)

                                                               tCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATctgcctg                                                   >  1:1109262/1‑139 (MQ=255)

                                                                       cTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTg                                           >  1:331387/1‑139 (MQ=255)

                                                                         cACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGaa                                         >  2:1056510/1‑139 (MQ=255)

                                                                         cACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGAGCCGATACGACGCCCACCTTCGTCACCTGCGGCGCCAGCTTGCGGAACGTACACAACGTGCCTGGCAGGCACTGCTGCGTTATCTACCTGCGGAAGTGaa                                         >  2:987525/1‑139 (MQ=255)

                                                                            cGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAAt                                      <  2:1196482/139‑1 (MQ=255)

                                                                            cGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAAt                                      <  2:91144/139‑1 (MQ=255)

                                                                            cGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAAt                                      <  1:806304/139‑1 (MQ=255)

                                                                                gCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATtcat                                  <  1:1105599/139‑1 (MQ=255)

                                                                                gCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATtcat                                  <  1:517946/139‑1 (MQ=255)

                                                                                gCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAACTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATtcat                                  <  2:337215/139‑1 (MQ=255)

                                                                                 cAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATtcatc                                 >  2:919431/1‑139 (MQ=255)

                                                                                      tGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCGCCTGCGTCGCCAGCTTGCGGaa                                                                                              >  2:694490/1‑73 (MQ=255)

                                                                                      tGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCGCCTGCGTCGCCAGCTTGCGGaa                                                                                              <  1:694490/73‑1 (MQ=255)

                                                                                        cgcTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGa                          <  2:1109262/139‑1 (MQ=255)

                                                                                          cTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGTCa                        <  1:919431/139‑1 (MQ=255)

                                                                                           tggtggATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAg                       <  2:1125893/139‑1 (MQ=255)

                                                                                              tggATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAGTgg                    >  1:793232/1‑139 (MQ=255)

                                                                                                  ttACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGt                                            >  2:502825/1‑111 (MQ=255)

                                                                                                  ttACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGt                                            <  1:502825/111‑1 (MQ=255)

                                                                                                  ttACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAGTGGTTAc                >  2:969795/1‑139 (MQ=255)

                                                                                                          ccACGCGCCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAGTGGTTACTTTCTCTg        >  1:23305/1‑139 (MQ=255)

                                                                                                               cgcCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCg                                                 >  2:877536/1‑93 (MQ=255)

                                                                                                               cgcCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCg                                                 <  1:877536/93‑1 (MQ=255)

                                                                                                                gcCGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAGTGGTTACTTTCTCTGGTTGGa  >  1:565280/1‑139 (MQ=255)

                                                                                                                 ccGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGc                                                                                                  >  2:461207/1‑42 (MQ=255)

                                                                                                                 ccGATACGACGCCCATCTTCGTCACCTGCGTCGCCAGCTTGc                                                                                                  <  1:461207/42‑1 (MQ=255)

                                                                                                                              cATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTggcagg                                                                        >  2:429954/1‑55 (MQ=255)

                                                                                                                              cATCTTCGTCACCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTggcagg                                                                        <  1:429954/55‑1 (MQ=255)

GGTTGGGTCGCCGCCGGAAAACATGCACGTAAAATTCAACGCTTGCAGTTGATGAGTACGCTTTCCACCAGCTCACCGATGCAACTTGCGCTGGTGGATTACCTTTCCACGCGCCGATACGACGCCCATCTTCGTCGCCTGCGTCGCCAGCTTGCGGAACGTAAACAACGTGCCTGGCAGGCACTGCTGCGTTATCTGCCTGCGGAAGTGAAAATTCATCATAATGACAGTGGTTACTTTCTCTGGTTGGA  >  NC_000913/1510963‑1511213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A