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	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,842,591	T→C	L151L (TTA→TTG)	hycI ←	protease involved in processing C‑terminal end of HycE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,842,591	0	T	C	97.4%	139.3 / ‑7.1	38	L151L (TTA→TTG)	hycI	protease involved in processing C‑terminal end of HycE
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/18); total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACTTC  >  NC_000913/2842465‑2842725

cGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAg                                                                                                                            <  2:343242/139‑1 (MQ=255)

             cccGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATttcctt                                                                                                               <  1:941555/139‑1 (MQ=255)

             cccGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATttcctt                                                                                                               >  1:920102/1‑139 (MQ=255)

                             caTCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCg                                                                                               <  1:873419/139‑1 (MQ=255)

                                                tGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAcc                                                                            <  1:3654/139‑1 (MQ=255)

                                                 ggCATCAGAGCTGGTTCACCCCATCAGGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCg                                                                           <  1:706020/139‑1 (MQ=255)

                                                 ggCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAg                                                                                                          >  2:508575/1‑108 (MQ=255)

                                                 ggCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAg                                                                                                          <  1:508575/108‑1 (MQ=255)

                                                            tGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATc                                                                <  1:487977/139‑1 (MQ=255)

                                                                 cACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTg                                                           <  2:685780/139‑1 (MQ=255)

                                                                   ccccATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTggg                                                         >  1:72674/1‑139 (MQ=255)

                                                                        tCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATc                                                    >  2:453837/1‑139 (MQ=255)

                                                                              aCATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGgtag                                              >  2:760938/1‑139 (MQ=255)

                                                                                 tCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaa                                           <  2:134175/139‑1 (MQ=255)

                                                                                  cccTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaaa                                          >  1:863634/1‑139 (MQ=255)

                                                                                  cccTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaaa                                          >  2:762121/1‑139 (MQ=255)

                                                                                    cTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGTCAAGCCGCCATTTCCTTCCCAGCCCTCCAGTCGTTGATAATCGGTTTCTACAGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAg                                        <  2:705808/139‑1 (MQ=255)

                                                                                      gTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGcc                                      >  1:920989/1‑139 (MQ=255)

                                                                                       tCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAg                                                                                                                            >  2:223083/1‑52 (MQ=255)

                                                                                       tCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAg                                                                                                                            <  1:223083/52‑1 (MQ=255)

                                                                                       tCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCa                                                      <  1:519935/122‑1 (MQ=255)

                                                                                       tCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCa                                                      >  2:519935/1‑122 (MQ=255)

                                                                                       tCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcg                                     >  1:333364/1‑139 (MQ=255)

                                                                                            aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCTATTTCCTTCCCAGCCTTCCAGTCGCTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTATTAAAAGCCGACGat                                >  2:680729/1‑139 (MQ=255)

                                                                                            aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGAGTAGTAAAAGCCGACGat                                >  1:673041/1‑139 (MQ=255)

                                                                                               ccTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATc                             <  1:865175/139‑1 (MQ=255)

                                                                                                 ttAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCAt                                                                        >  2:192982/1‑94 (MQ=255)

                                                                                                 ttAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCAt                                                                        <  1:192982/94‑1 (MQ=255)

                                                                                                      gAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTccc                                                                                                            <  1:225925/53‑1 (MQ=255)

                                                                                                      gAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTccc                                                                                                            >  2:225925/1‑53 (MQ=255)

                                                                                                       aaaaaCTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGaa                     >  1:613456/1‑139 (MQ=255)

                                                                                                          aaCTACTCTTCTTCCGCCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCCTCGGGTAGTAGTAGCCGACGATATCCGGCTGAATGc                  <  1:682926/139‑1 (MQ=255)

                                                                                                               ctctTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcgac                                   <  2:379245/117‑1 (MQ=255)

                                                                                                               ctctTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcgac                                   >  1:379245/1‑117 (MQ=255)

                                                                                                               ctctTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAgg             >  1:1088563/1‑139 (MQ=255)

                                                                                                                        cACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACt    <  1:16351/139‑1 (MQ=255)

                                                                                                                        cACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACt    <  2:1088563/139‑1 (MQ=255)

                                                                                                                          ccGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACTTc  >  2:974680/1‑139 (MQ=255)

CGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACTTC  >  NC_000913/2842465‑2842725

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