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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,884,215 T→C 25.6% A131A (GCA→GCG)  cpdB ← 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,884,2150TC25.6% 131.4 / 43.2 113A131A (GCA→GCG) cpdB2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase
Reads supporting (aligned to +/- strand):  ref base T (39/45);  new base C (16/13);  total (55/58)
Fisher's exact test for biased strand distribution p-value = 5.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 114 total aligned reads displayed.

AACATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTA  >  minE/2884153‑2884281
                                                              |                                                                   
aaCATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAg                                                                >  1:3430864/1‑68 (MQ=255)
aaCATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAg                                                                >  1:2697997/1‑68 (MQ=255)
aaCATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAg                                                                >  1:2270418/1‑68 (MQ=255)
aaCATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAg                                                                >  1:143650/1‑68 (MQ=255)
aaCATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAg                                                                >  1:1210456/1‑68 (MQ=255)
         tGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTc                                                     <  1:3002649/69‑1 (MQ=255)
                          aaTGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTa                                    >  1:691740/1‑69 (MQ=255)
                              aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:2699372/69‑1 (MQ=255)
                              aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:1449549/69‑1 (MQ=255)
                              aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:2355411/69‑1 (MQ=255)
                              aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:1583995/69‑1 (MQ=255)
                              aCGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:579496/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCTCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:2248782/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:889106/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:2030050/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:3100550/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:3403236/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:1874056/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:45748/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:1741061/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:1581303/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:2453136/69‑1 (MQ=255)
                                 ttGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:2482035/69‑1 (MQ=255)
                                  tGGCATTTACATAAGGGAATTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAAc                             <  1:1327225/68‑1 (MQ=255)
                                   ggCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGt                                     >  1:2158928/1‑59 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGt                                                 >  1:2923329/1‑41 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGt                                                 >  1:807538/1‑41 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGt                                                 >  1:319060/1‑41 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2818508/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2804854/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2923648/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2734686/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2634381/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2157527/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:2560452/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:651350/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:687345/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:1481373/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:713073/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:1415743/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:1388624/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:130886/1‑69 (MQ=255)
                                         tACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGtt                     >  1:804895/1‑69 (MQ=255)
                                               aGGGAATTTCGCTCCTGCCAGCGCATTTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCaa                >  1:2503444/1‑69 (MQ=255)
                                               aGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:520419/52‑1 (MQ=255)
                                               aGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTg                        >  1:2086780/1‑60 (MQ=255)
                                                 ggAATTTCGCTCCTGCCAGCTCA‑TTTTTCAGGTAATCCAGACCGTAGTTa                                <  1:790752/50‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:2628293/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            >  1:2611849/1‑69 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:3079099/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:3418441/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:813984/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:1021171/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:1671954/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:1937481/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGt            <  1:1956058/69‑1 (MQ=255)
                                                  gAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGAGGTTGCCAAGCGt            <  1:757372/69‑1 (MQ=255)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACtt                           >  1:2077093/1‑51 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACt                            >  1:186667/1‑51 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:2865100/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:1034355/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:850205/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:1260814/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:1305044/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:671686/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:548395/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:523283/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:385552/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:377486/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:1905284/1‑52 (MQ=39)
                                                    aTTTCGCTCCCGCCAGCGCA‑TTTTTCAGATAATCCAGACCGTAGTTAAACTc                           >  1:2492044/1‑52 (MQ=39)
                                                      ttCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg        >  1:3261968/1‑69 (MQ=255)
                                                      ttCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg        >  1:3374398/1‑69 (MQ=255)
                                                      ttCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg        >  1:309382/1‑69 (MQ=255)
                                                      ttCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg        >  1:2669869/1‑69 (MQ=255)
                                                      ttCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCg        >  1:2030957/1‑69 (MQ=255)
                                                           tCCTGCGAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:3070933/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:2556839/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:814191/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:1046551/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:2225422/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:1347055/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:1619617/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:2429053/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:1894224/68‑1 (MQ=255)
                                                           tCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:1820988/68‑1 (MQ=255)
                                                           tCCTGACAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:161665/68‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:1459735/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:2345146/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:2906317/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:2623682/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:2205241/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:308268/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:438519/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:1576202/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:2412847/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:1836710/69‑1 (MQ=255)
                                                            ccTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:3132839/69‑1 (MQ=255)
                                                             cTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGta  <  1:673243/68‑1 (MQ=255)
                                                              tGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACgg    <  1:497550/65‑1 (MQ=255)
                                                              |                                                                   
AACATTGGCTGTTTGGTTCTGGCGTCAATGACGTTGGCATTTACATAAGGGAATTTCGCTCCTGCCAGCGCA‑TTTTTCAGGTAATCCAGACCGTAGTTAAACTCGTGGTTGCCAAGCGTTCCGACGGTA  >  minE/2884153‑2884281

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A