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
A5 F1 I2 R1	77	34.8	1608548	95.0%	1528120	114.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,771,806	A→T	intergenic (+191/+196)	yfjT → / ← yfjU	CP4‑57 prophage, putative periplasmic protein/CP4‑57 prophage, conserved protein,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,771,806	0	A	T	94.6%	120.1 / ‑0.3	37	intergenic (+191/+196)	yfjT/yfjU	CP4‑57 prophage, putative periplasmic protein/CP4‑57 prophage, conserved protein,Phage or Prophage Related
Reads supporting (aligned to +/- strand): ref base A (0/2); new base T (17/18); total (17/20)
Fisher's exact test for biased strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01

AGAGGTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGATCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATATGAATGAATACTGCGGATATCAACATGGCCAAT  >  NC_000913/2771691‑2771932

agagGTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATgg                                                                                                         >  2:363472/1‑139 (MQ=255)

agagGTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATgg                                                                                                         >  2:187302/1‑139 (MQ=255)

agagGTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATgg                                                                                                         <  1:363472/139‑1 (MQ=255)

    gTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGGTGTATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTc                                                                                                                              >  1:795514/1‑114 (MQ=255)

    gTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTc                                                                                                                              <  2:795514/114‑1 (MQ=255)

    gTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTc                                                                                                     >  2:708598/1‑139 (MQ=255)

     tAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCa                                                                                                    <  1:315735/139‑1 (MQ=255)

     tAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGATCACTTTTTGGTCTAAGCGATGGTTTCa                                                                                                    <  2:494685/139‑1 (MQ=255)

       ggCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGa                                                                                                            <  2:674368/129‑1 (MQ=255)

       ggCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGa                                                                                                            >  1:674368/1‑129 (MQ=255)

       ggCCACGTACTTTCGAACGATGAGCGCAGAGGTCAGTTTTTTTCACATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCata                                                                                                  >  1:462521/1‑139 (MQ=255)

              tACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGt                                                                                                                    <  1:44816/114‑1 (MQ=255)

              tACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGt                                                                                                                    >  2:44816/1‑114 (MQ=255)

               aCTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAAc                                                                                          <  1:104561/139‑1 (MQ=255)

               aCTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAAc                                                                                          <  1:187302/139‑1 (MQ=255)

                          aTGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATa                                                                               <  1:798795/139‑1 (MQ=255)

                          aTGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATa                                                                               <  2:597613/139‑1 (MQ=255)

                           tGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGATCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATaa                                                                              <  1:278559/139‑1 (MQ=255)

                                    tGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATgag                                                                     <  1:708598/139‑1 (MQ=255)

                                                     atatatTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTGAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCa                                                    >  1:656138/1‑139 (MQ=255)

                                                     atatatTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCAtt                                                                                      >  2:16543/1‑105 (MQ=255)

                                                     atatatTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCAtt                                                                                      <  1:16543/105‑1 (MQ=255)

                                                                  tttttGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTaaaaa                                       >  2:657644/1‑139 (MQ=255)

                                                                      tGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGata                                   <  2:462521/139‑1 (MQ=255)

                                                                          tGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATatgaa                               >  1:437764/1‑139 (MQ=255)

                                                                              aGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGa                                     <  1:345616/129‑1 (MQ=255)

                                                                              aGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGa                                     >  2:345616/1‑129 (MQ=255)

                                                                                            cgcAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATatgaat                              >  2:660618/1‑122 (MQ=255)

                                                                                            cgcAGGCTGTGTTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATatgaat                              <  1:660618/122‑1 (MQ=255)

                                                                                                    gtgtTAAAACTCCTGTTCACTTTTTGGTCTAAGCg                                                                                                             >  1:597666/1‑35 (MQ=37)

                                                                                                    gtgtTAAAACTCCTGTTCACTTTTTGGTCTAAGCg                                                                                                             <  2:597666/35‑1 (MQ=255)

                                                                                                    gtgtTAAAACTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCAtt                                                                                      <  2:537271/58‑1 (MQ=255)

                                                                                                    gtgtTAAAACGCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCAtt                                                                                      >  1:537271/1‑58 (MQ=255)

                                                                                                           aaCTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATATGAATGAATACTGCGGATATCAACATGGCCAAt  <  2:653615/135‑1 (MQ=255)

                                                                                                           aaCTCCTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATATGAATGAATACTGCGGATATCAACATGGCCAAt  >  1:653615/1‑135 (MQ=255)

                                                                                                               ccTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAAccc                                                                          >  1:59482/1‑59 (MQ=255)

                                                                                                               ccTGTTCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAAccc                                                                          <  2:59482/59‑1 (MQ=255)

AGAGGTAGGCCACGTACTTTCGAACGATGAGCGCAGTGGTCAGTTTTTTTCAGATATATTTATCTTTTTTTGGCTGTAAGCTCCGCTGTGAGCGCAGGCTGTGTTAAAACTCCTGATCACTTTTTGGTCTAAGCGATGGTTTCATATGATCAACCATTCTTGATAAACCCATGAGACGGACTAACTTTTTCATTAAAATTAAAAAGATATGAATGAATACTGCGGATATCAACATGGCCAAT  >  NC_000913/2771691‑2771932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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