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
A17 F48 I1 R1	90	35.3	1199032	98.5%	1181046	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	800,423	C→A	E51D (GAG→GAT)	ybhD ←	putative DNA‑binding transcriptional regulator YbhD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	800,423	0	C	A	90.5%	121.9 / 7.3	42	E51D (GAG→GAT)	ybhD	putative DNA‑binding transcriptional regulator YbhD
Reads supporting (aligned to +/- strand): ref base C (2/2); new base A (18/20); total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACGTCACCATACCACGATGATAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGCTCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGACAAATGCCTTCATA  >  NC_000913/800286‑800555

aaCGTCACCATACCACGATGATAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATc                                                                                                                                    >  1:281051/1‑140 (MQ=255)

  cGTCACCATACCACGATGATAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCaa                                                                                                                                  >  1:582678/1‑140 (MQ=255)

                gatgatAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGt                                                                                                                    <  2:281051/140‑1 (MQ=255)

                  tgatAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGCTCAAATAGTTGAACATGTaa                                                                                                                  >  2:427211/1‑140 (MQ=255)

                    atAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGCTCAAATAGTTGAACATGTAAAt                                                                                                                >  2:268283/1‑140 (MQ=255)

                      aaGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCt                                                                                                              >  2:168153/1‑140 (MQ=255)

                       aGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAATTAGTTGAACATGTAAATCtt                                                                                                             >  2:34884/1‑140 (MQ=255)

                          aTTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTtcct                                                                                                          >  1:529620/1‑140 (MQ=255)

                            tCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTtcctcc                                                                                                        >  1:272553/1‑140 (MQ=255)

                              atatCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCAt                                                                                                      <  2:283688/140‑1 (MQ=255)

                                      aaTATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTa                                                                                              >  1:215951/1‑140 (MQ=255)

                                      aaTATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTa                                                                                              >  2:443569/1‑140 (MQ=255)

                                        tatTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTAtt                                                                                            >  2:144588/1‑140 (MQ=255)

                                           tAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTAttctt                                                                                         <  2:68942/140‑1 (MQ=255)

                                               aaGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGCTCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTcgcg                                                                                     <  1:268283/140‑1 (MQ=255)

                                               aaGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTcgcg                                                                                     <  2:70859/140‑1 (MQ=255)

                                                    tttCATCGAATTTCTTTATTAATTCCCGTGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAAt                                                                                >  1:506892/1‑140 (MQ=255)

                                                    tttCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAAt                                                                                >  2:394933/1‑140 (MQ=255)

                                                    tttCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAAt                                                                                >  2:587316/1‑140 (MQ=255)

                                                    tttCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAAt                                                                                >  1:576278/1‑140 (MQ=255)

                                                    tttCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAAt                                                                                >  1:103913/1‑140 (MQ=255)

                                                         tCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAgg                                                                           <  2:536981/140‑1 (MQ=255)

                                                         tCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAgg                                                                           <  2:64544/140‑1 (MQ=255)

                                                         tCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAgg                                                                           <  1:587316/140‑1 (MQ=255)

                                                         tCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAgg                                                                           <  1:443569/140‑1 (MQ=255)

                                                              tttCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCg                                                                      <  2:200340/140‑1 (MQ=255)

                                                              tttCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCg                                                                      <  1:44656/140‑1 (MQ=255)

                                                                   ttattaATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAata                                                                 <  1:144588/140‑1 (MQ=255)

                                                                    tattaATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAatat                                                                >  1:397450/1‑140 (MQ=255)

                                                                         aTTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGt                                                           <  1:492909/140‑1 (MQ=255)

                                                                                     ccGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGCTCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCa                                               <  1:162351/140‑1 (MQ=255)

                                                                                            cAACCTTTTTCCTGCTTTTGTTAACGTATCCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAGTGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTag                                        <  2:575213/140‑2 (MQ=255)

                                                                                             aaCCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTaaa                                       >  1:42588/1‑140 (MQ=255)

                                                                                                 tttttCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGaa                                   <  2:576278/140‑1 (MQ=255)

                                                                                                    ttCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTg                                >  1:434877/1‑140 (MQ=255)

                                                                                                    ttCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTg                                >  2:145071/1‑140 (MQ=255)

                                                                                                         gCTTTTGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGActc                           >  1:11623/1‑140 (MQ=255)

                                                                                                            tttGTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGc                        <  1:357438/140‑1 (MQ=255)

                                                                                                               gTTAACGTAACCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAg                     <  1:12478/140‑1 (MQ=255)

                                                                                                                        aCCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGTCaaa            <  2:397450/140‑1 (MQ=255)

                                                                                                                        aCCTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGACaaa            <  2:529620/140‑1 (MQ=255)

                                                                                                                         ccTTGCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGACAAAt           <  2:506892/140‑1 (MQ=255)

                                                                                                                             gCGAGTTGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGACAAATGCCt       <  1:145071/140‑1 (MQ=255)

                                                                                                                                  ttGTACGATCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGACAAATGCCTTCATa  <  1:34884/140‑1 (MQ=255)

AACGTCACCATACCACGATGATAAGCATTCATATCACGAATATTAAAAAGCGTTTCATCGAATTTCTTTATTAATTCCCGCGCCTCCGGGAGCAACCTTTTTCCTGCTTTTGTTAACGTAACCTTGCGAGTTGTACGCTCAAATAGTTGAACATGTAAATCTTCCTCCATCTTTTTTATTCTTCGCGTTAATGCAGGTTGCGTAATATTGAGTAATTTAGCGGCATTGTTAAACGAACTGGACTCTGCCAGTATGACAAATGCCTTCATA  >  NC_000913/800286‑800555

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A